SOYBEAN EVENT DP-305423-1 AND COMPOSITIONS AND METHODS FOR THE IDENTIFICATION AND/OR DETECTION THEREOF
Compositions and methods related to transgenic high oleic acid/ALS inhibitor-tolerant soybean plants are provided. Specifically, the present invention provides soybean plants having a DP-305423-1 event which imparts a high oleic acid phenotype and tolerance to at least one ALS-inhibiting herbicide. The soybean plant harboring the DP-305423-1 event comprises genomic/transgene junctions having at least the polynucleotide sequence of SEQ ID NO:8, 9, 14, 15, 20, 21, 83 or 84. The characterization of the genomic insertion site of the DP-305423-1 event provides for an enhanced breeding efficiency and enables the use of molecular markers to track the transgene insert in the breeding populations and progeny thereof. Various methods and compositions for the identification, detection, and use of the soybean DP-305423-1 events are provided.
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This application is a continuation of U.S. patent application Ser. No. 16/927,472 filed Jul. 13, 2020, which is a divisional of U.S. patent application Ser. No. 15/786,627, filed Oct. 18, 2017, now U.S. Pat. No. 10,745,711, which is a divisional of U.S. patent application Ser. No. 14/053,059, filed Oct. 14, 2013, now U.S. Pat. No. 9,816,098, which is a continuation of U.S. patent application Ser. No. 11/927,894, filed Oct. 30, 2007, now U.S. Pat. No. 8,609,935, which claims the benefit of U.S. Provisional App. No. 60/863,721, filed Oct. 31, 2006 and U.S. Provisional App. No. 60/942,676, filed Jun. 8, 2007, the entire contents of each of which are herein incorporated by reference.
REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLYThe official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file named BB1594-US-DIV[2]_SubstituteSeqLst.txt created on Feb. 23, 2022 and having a size of 152 kilobytes and is filed concurrently with the specification. The sequence listing contained in this ASCII formatted document is part of the specification and is herein incorporated by reference in its entirety.
FIELD OF THE INVENTIONThis invention is in the field of molecular biology. More specifically, this invention pertains to plants that display both a high oleic acid phenotype and a herbicide tolerance phenotype conferred by suppression of a FAD2 gene in conjunction with the expression of a sequence that confers tolerance to inhibitors of ALS.
BACKGROUND OF THE INVENTIONThe expression of foreign genes in plants is known to be influenced by their location in the plant genome, perhaps due to chromatin structure (e.g., heterochromatin) or the proximity of transcriptional regulatory elements (e.g., enhancers) close to the integration site (Weising et al. (1988) Ann. Rev. Genet 22: 421-477). At the same time the presence of the transgene at different locations in the genome influences the overall phenotype of the plant in different ways. For this reason, it is often necessary to screen a large number of events in order to identify an event characterized by optimal expression of an introduced gene of interest. For example, it has been observed in plants and in other organisms that there may be a wide variation in levels of expression of an introduced gene among events. There may also be differences in spatial or temporal patterns of expression, for example, differences in the relative expression of a transgene in various plant tissues, that may not correspond to the patterns expected from transcriptional regulatory elements present in the introduced gene construct. It is also observed that the transgene insertion can affect the endogenous gene expression. For these reasons, it is common to produce hundreds to thousands of different events and screen those events for a single event that has desired transgene expression levels and patterns for commercial purposes. An event that has desired levels or patterns of transgene expression is useful for introgressing the transgene into other genetic backgrounds by sexual outcrossing using conventional breeding methods. Progeny of such crosses maintain the transgene expression characteristics of the original transformant. This strategy is used to ensure reliable gene expression in a number of varieties that are well adapted to local growing conditions.
It would be advantageous to be able to detect the presence of a particular event in order to determine whether progeny of a sexual cross contain a transgene of interest. In addition, a method for detecting a particular event would be helpful for complying with regulations requiring the pre-market approval and labeling of foods derived from recombinant crop plants, or for use in environmental monitoring, monitoring traits in crops in the field, or monitoring products derived from a crop harvest, as well as, for use in ensuring compliance of parties subject to regulatory or contractual terms.
In the commercial production of crops, it is desirable to easily and quickly eliminate unwanted plants (i.e., “weeds”) from a field of crop plants. An ideal treatment would be one which could be applied to an entire field but which would eliminate only the unwanted plants while leaving the crop plants unharmed. One such treatment system would involve the use of crop plants which are tolerant to a herbicide so that when the herbicide was sprayed on a field of herbicide-tolerant crop plants, the crop plants would continue to thrive while non-herbicide-tolerant weeds were killed or severely damaged.
Plant lipids find their major use as edible oils in the form of triacylglycerols. The specific performance and health attributes of edible oils are determined largely by their fatty acid composition. Most vegetable oils derived from commercial plant varieties are composed primarily of palmitic (16:0), stearic (18:0), oleic (18:1), linoleic (18:2) and linolenic (18:3) acids. Palmitic and stearic acids are, respectively, 16- and 18-carbon-long, saturated fatty acids. Oleic, linoleic, and linolenic acids are 18-carbon-long, unsaturated fatty acids containing one, two, and three double bonds, respectively. Oleic acid is referred to as a mono-unsaturated fatty acid, while linoleic and linolenic acids are referred to as poly-unsaturated fatty acids.
A vegetable oil low in total saturates and high in mono-unsaturates would provide significant health benefits to consumers as well as economic benefits to oil processors. As an example, canola oil is considered a very healthy oil. However, in use, the high level of poly-unsaturated fatty acids in canola oil renders the oil unstable, easily oxidized, and susceptible to development of disagreeable odors and flavors (Gailliard, 1980, Vol. 4, pp. 85-116 In: Stumpf, P. K., Ed., The Biochemistry of Plants, Academic Press, New York). The levels of poly-unsaturates may be reduced by hydrogenation, but the expense of this process and the concomitant production of nutritionally questionable trans isomers of the remaining unsaturated fatty acids reduces the overall desirability of the hydrogenated oil (Mensink et al., New England J. Medicine (1990) N323: 439-445). Similar problems exist with soybean and corn oils.
SUMMARY OF THE INVENTIONCompositions and methods related to transgenic high oleic acid/ALS inhibitor-tolerant soybean plants are provided. Specifically, the present invention provides soybean plants containing a DP-305423-1 event which imparts a high oleic acid phenotype and tolerance to at least one ALS-inhibiting herbicide. The soybean plant harboring the DP-305423-1 event at the recited chromosomal location comprises genomic/transgene junctions having at least the polynucleotide sequence of SEQ ID NO:8, 9, 14, 15, 20, 21, 83 or 84. The characterization of the genomic insertion site of the DP-305423-1 event provides for an enhanced breeding efficiency and enables the use of molecular markers to track the transgene insert in the breeding populations and progeny thereof. Various methods and compositions for the identification, detection, and use of the soybean DP-305423-1 event are provided.
In one embodiment, the present invention includes an isolated polynucleotide comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88.
In another embodiment, the present invention includes a soybean plant or a soybean seed comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88.
In another embodiment, the present invention includes a method for identifying a biological sample comprising: a) contacting said biological sample with a first and a second primer; b) amplifying a polynucleotide comprising any of SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88; and c) confirming said biological sample comprises a polynucleotide comprising any of SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88. The method may further comprise detecting a polynucleotide comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88 by hybridization to a probe, wherein said probe hybridizes under stringent hybridization conditions with a polynucleotide comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88. The first or second primer may comprise a fragment of a 5′ genomic region, a 3′ genomic region or an insert region of SEQ ID NO:5, 6, 7 or 82. The first or second primer may comprise at least 8 consecutive nucleotides of a 5′ genomic region, a 3′ genomic region or an insert region of SEQ ID NO:5, 6, 7 or 82. One of the first or second primers may comprise a fragment of a 5′ genomic region of SEQ ID NO:5, 6, 7 or 82 and the other of the first or second primers may comprise a fragment of a 3′ genomic region of SEQ ID NO:5, 6, 7 or 82. The first or second primer may comprise SEQ ID NO:26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 89, or 90.
In another embodiment, the present invention includes a method of detecting the presence of a polynucleotide comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88 in a biological sample comprising DNA, comprising: (a) extracting a DNA sample from said biological sample; (b) contacting said DNA sample with at least one pair of DNA primer molecules selected from the group consisting of: i) the sequences comprising SEQ ID NO:26 and SEQ ID NO:27; ii) the sequences comprising SEQ ID NO:29 and SEQ ID NO:30; iii) the sequences comprising SEQ ID NO:31 and SEQ ID NO:32; iv) the sequences comprising SEQ ID NO:33 and SEQ ID NO:32; v) the sequences comprising SEQ ID NO:35 and SEQ ID NO:36; vi) the sequences comprising SEQ ID NO:37 and SEQ ID NO:38; vii) the sequences comprising SEQ ID NO:39 and SEQ ID NO:40; viii) the sequences comprising SEQ ID NO:41 and SEQ ID NO:42; ix) the sequences comprising SEQ ID NO:43 and SEQ ID NO:44; x) the sequences comprising SEQ ID NO:45 and SEQ ID NO:46; xi) the sequences comprising SEQ ID NO:47 and SEQ ID NO:48; xii) the sequences comprising SEQ ID NO:47 and SEQ ID NO:49; xiii) the sequences comprising SEQ ID NO:50 and SEQ ID NO:51; xiv) the sequences comprising SEQ ID NO:52 and SEQ ID NO:53; xv) the sequences comprising SEQ ID NO:54 and SEQ ID NO:49; xvi) the sequences comprising SEQ ID NO:55 and SEQ ID NO:46; xvii) the sequences comprising SEQ ID NO:33 and SEQ ID NO:56; xviii) the sequences comprising SEQ ID NO:57 and SEQ ID NO:58; xix) the sequences comprising SEQ ID NO:59 and SEQ ID NO:60; xx) the sequences comprising SEQ ID NO:61 and SEQ ID NO:36; xxi) the sequences comprising SEQ ID NO:35 and SEQ ID NO:62; xxii) the sequences comprising SEQ ID NO:37 and SEQ ID NO:63; xxiii) the sequences comprising SEQ ID NO:64 and SEQ ID NO:65; xxiv) the sequences comprising SEQ ID NO:66 and SEQ ID NO:67; xxv) the sequences comprising SEQ ID NO:68 and SEQ ID NO:69; xxvi) the sequences comprising SEQ ID NO:70 and SEQ ID NO:71; xxvii) the sequences comprising SEQ ID NO:72 and SEQ ID NO:73; xxviii) the sequences comprising SEQ ID NO:74 and SEQ ID NO:75; xxix) the sequences comprising SEQ ID NO:76 and SEQ ID NO:77; xxx) the sequences comprising SEQ ID NO:78 and SEQ ID NO:79; xxxi) the sequences comprising SEQ ID NO:80 and SEQ ID NO:81; and xxxii) the sequences comprising SEQ ID NO:89 and SEQ ID NO:90 (c) providing DNA amplification reaction conditions; (d) performing said DNA amplification reaction, thereby producing a DNA amplicon molecule; and (e) detecting said DNA amplicon molecule, wherein the detection of said DNA amplicon molecule in said DNA amplification reaction indicates the presence of a polynucleotide comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88.
In another embodiment, the present invention includes a method of detecting the presence of SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88 in a biological sample, the method comprising: (a) contacting the biological sample comprising DNA under stringent hybridization conditions with a polynucleotide probe wherein said probe hybridizes under stringent hybridization conditions with a polynucleotide comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88; (b) detecting hybridization of the probe to the DNA. The biological sample may comprise soybean tissue.
In another embodiment, the present invention includes an isolated DNA primer comprising at least one sequence selected from the group consisting of SEQ ID NO:26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 89, or 90 or its complement.
In another embodiment, the present invention includes a pair of DNA primers comprising a first DNA primer and a second DNA primer, wherein the DNA primers are of a sufficient length of contiguous nucleotides of SEQ ID NO:5, 6, 7 or 82, to function as DNA primers diagnostic of DNA comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88.
In another embodiment, the present invention includes a DNA probe wherein the DNA probe is of a sufficient length of contiguous nucleotides of SEQ ID NO:5, 6, 7 or 82, to function as a DNA probe diagnostic of DNA comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88.
In another embodiment, the present invention includes a method for screening seed for a polynucleotide comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88, comprising: a) contacting a sample comprising DNA from said seed with a first and a second DNA primer; b) amplifying a polynucleotide comprising a polynucleotide comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88; and c) detecting said amplified polynucleotide.
In another embodiment, the present invention includes a method for screening seed for the presence of a polynucleotide comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88 comprising: (a) contacting a sample comprising DNA from said seed under stringent hybridization conditions with a polynucleotide probe that hybridizes under stringent hybridization conditions with a polynucleotide comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88; and (b) detecting hybridization of the probe to the DNA.
In another embodiment, the present invention includes a method of producing a high oleic acid and ALS inhibitor tolerant plant comprising breeding a plant comprising a polynucleotide comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88, and selecting progeny by analyzing for progeny that comprise a polynucleotide comprising SEQ ID NO: 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88.
In another embodiment, the present invention includes an isolated DNA sequence comprising at least one nucleotide sequence selected from the group consisting of: (a) a nucleotide sequence set forth in SEQ ID NO:26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 89, or 90; and (b) a full-length complement of the nucleotide sequence of (a).
In another embodiment, the present invention includes a pair of isolated DNA primer sequences, each comprising at least ten nucleotides and which when used together in a DNA amplification procedure will produce a DNA amplicon comprising a polynucleotide comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88. The pair of isolated DNA primer sequences may comprise a first primer sequence chosen from the group consisting of: a) a 5′ genomic region of SEQ ID NO: 5, 6, 7 or 82; and b) a 3′ genomic region of SEQ ID NO: 5, 6, 7 or 82; and a second primer sequence chosen from an insert region of SEQ ID NO: 5, 6, 7 or 82.
In another embodiment, the present invention includes a method for controlling weeds in an area of cultivation comprising applying an effective amount of an ALS inhibitor to the area of cultivation comprising soybean plants comprising a polynucleotide comprising SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88. The ALS inhibitor may be a sulfonylurea herbicide or an imidazolinone herbicide. A combination of different ALS inhibitors may be used. The ALS inhibitor or combination of ALS inhibitors may be used in further combination with one or more non-ALS inhibitor herbicides.
In another embodiment, the present invention includes a DNA expression construct comprising the isolated polynucleotide of the invention operably linked to at least one regulatory sequence.
In another embodiment, the present invention includes transgenic progeny plants obtained from the transgenic seed of the invention.
In another embodiment, the present invention includes a recombinant DNA construct comprising: a first and second expression cassette, wherein said first expression cassette in operable linkage comprises: (a) a soybean KTi3 promoter; (b) a gm-fad2-1 fragment; and (c) a soybean KTi3 transcriptional terminator; and said second expression cassette comprises in operable linkage: (i) a soybean SAMS promoter; (ii) a soybean SAMS 5′ untranslated leader and intron; (iii) a soybean gm-hra encoding DNA molecule; and (iv) a soybean als transcriptional terminator.
In another embodiment, the present invention includes a plant or seed comprising the recombinant DNA construct of claim 27. The plant or seed may be a soybean plant or a soybean seed.
Table 1 presents a description of the following sequences that are present in the Sequence Listing: (1) the insert sequences used to create the DP-305423-1 event and the vectors from which they are derived; (2) the genomic DNA sequences present in Contig-1, Contig-2, Contig-3 and Contig-4; (3) the 5′ and 3′ junction sequences, at which transgenic insert and endogenous soybean genomic sequence are joined, for each of the four contigs; and (4) primer sequences that can be used to amply 5′ and 3′ junction sequences from each of the four contigs.
The present inventions now will be described more fully hereinafter with reference to the accompanying drawings, in which some, but not all embodiments of the inventions are shown. Indeed, these inventions may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements.
Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.
The following abbreviations are used in describing the present invention.
-
- ALS acetolactate synthase protein
- bp base pair
- FAD2 microsomal omega-6 desaturase protein
- gm-fad2-1 soybean microsomal omega-6 desaturase gene 1
- gm-als wild type acetolactate synthase gene from soybean
- gm-hra modified version of acetolactate synthase gene from soybean
- kb kilobase
- PCR polymerase chain reaction
- UTR untranslated region
Compositions and methods related to transgenic high oleic acid/ALS inhibitor-tolerant soybean plants are provided. Specifically, the present invention provides soybean plants having event DP-305423-1. A soybean plant having “event DP-305423-1” has been modified by the insertion of a suppression cassette containing a 597 bp fragment of the soybean microsomal omega-6 desaturase gene 1 (gm-fad2-1) and an expression cassette containing a modified version of the soybean acetolactate synthase gene (gm-hra). The insertion of the gm-fad2-1 suppression cassette in the plant confers a high oleic acid phenotype. The insertion of the gm-hra gene produces a modified form of the acetolactate synthase (ALS) enzyme. ALS is essential for branched chain amino acid biosynthesis and is inhibited by certain herbicides. The modification in the gm-hra gene overcomes this inhibition and thus provides tolerance to a wide range of ALS-inhibiting herbicides. Thus, a soybean plant having a DP-305423-1 event has a high oleic acid phenotype and is tolerant at least one ALS-inhibiting herbicide.
The polynucleotides conferring the high oleic acid phenotype and ALS inhibitor tolerance are genetically linked in the soybean genome in the DP-305423-1 soybean event. The soybean plant harboring the DP-305423-1 event comprises genomic/transgene junctions having at least the polynucleotide sequence of SEQ ID NO: 8, 9, 14, 15, 20, 21, 83, and 84. The characterization of the genomic insertion site of the DP-305423-1 event provides for an enhanced breeding efficiency and enables the use of molecular markers to track the transgene insert in the breeding populations and progeny thereof. Various methods and compositions for the identification, detection, and use of the soybean DP-305423-1 events are provided herein. As used herein, the term “event DP-305423-1 specific” refers to a polynucleotide sequence which is suitable for discriminatively identifying event DP-305423-1 in plants, plant material, or in products such as, but not limited to, food or feed products (fresh or processed) comprising, or derived from plant material.
As used herein, the term “soybean” means Glycine max and includes all plant varieties that can be bred with soybean. As used herein, the term plant includes plant cells, plant organs, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruit, stalks, roots, root tips, anthers, and the like. Grain is intended to mean the mature seed produced by commercial growers for purposes other than growing or reproducing the species. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise a DP-305423-1 event.
A transgenic “event” is produced by transformation of plant cells with a heterologous DNA construct(s), including a nucleic acid expression cassette that comprises a transgene of interest, the regeneration of a population of plants resulting from the insertion of the transgene into the genome of the plant, and selection of a particular plant characterized by insertion into a particular genome location. An event is characterized phenotypically by the expression of the transgene(s). At the genetic level, an event is part of the genetic makeup of a plant. The term “event” also refers to progeny produced by a sexual outcross between the transformant and another variety that include the heterologous DNA. Even after repeated back-crossing to a recurrent parent, the inserted DNA and flanking DNA from the transformed parent is present in the progeny of the cross at the same chromosomal location. The term “event” also refers to DNA from the original transformant comprising the inserted DNA and flanking sequence immediately adjacent to the inserted DNA that would be expected to be transferred to a progeny that receives inserted DNA including the transgene of interest as the result of a sexual cross of one parental line that includes the inserted DNA (e.g., the original transformant and progeny resulting from selfing) and a parental line that does not contain the inserted DNA.
As used herein, “insert DNA” refers to the heterologous DNA within the expression cassettes used to transform the plant material while “flanking DNA” can comprise either genomic DNA naturally present in an organism such as a plant, or foreign (heterologous) DNA introduced via the transformation process which is extraneous to the original insert DNA molecule, e.g. fragments associated with the transformation event. A “flanking region” or “flanking sequence” as used herein refers to a sequence of at least 20, 50, 100, 200, 300, 400, 1000, 1500, 2000, 2500, or 5000 base pair or greater which is located either immediately upstream of and contiguous with or immediately downstream of and contiguous with the original foreign insert DNA molecule. Non-limiting examples of the flanking regions of the DP-305423-1 event are set forth in SEQ ID NO:5, 6, 7 and 82, and variants and fragments thereof.
Transformation procedures leading to random integration of the foreign DNA will result in transformants containing different flanking regions characteristic of and unique for each transformant. A “junction” is a point where two specific DNA fragments join. For example, a junction exists where insert DNA joins flanking genomic DNA. A junction point also exists in a transformed organism where two DNA fragments join together in a manner that is modified from that found in the native organism. As used herein, “junction DNA” refers to DNA that comprises a junction point. Non-limiting examples of junction DNA from the DP-305423-1 event set are forth in SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88, or variants and fragments thereof.
A DP-305423-1 plant can be bred by first sexually crossing a first parental soybean plant grown from the transgenic DP-305423-1 soybean plant (or progeny thereof derived from transformation with the expression cassettes of the embodiments of the present invention that confer herbicide tolerance) and a second parental soybean plant that lacks the herbicide tolerance phenotype, thereby producing a plurality of first progeny plants; and then selecting a first progeny plant that displays the desired herbicide tolerance; and selfing the first progeny plant, thereby producing a plurality of second progeny plants; and then selecting from the second progeny plants which display the desired herbicide tolerance. These steps can further include the back-crossing of the first herbicide tolerant progeny plant or the second herbicide tolerant progeny plant to the second parental soybean plant or a third parental soybean plant, thereby producing a soybean plant that displays the desired herbicide tolerance. It is further recognized that assaying progeny for phenotype is not required. Various methods and compositions, as disclosed elsewhere herein, can be used to detect and/or identify the DP-305423-1 event.
It is also to be understood that two different transgenic plants can also be mated to produce offspring that contain two independently segregating added, exogenous genes. Selfing of appropriate progeny can produce plants that are homozygous for both added, exogenous genes. Back-crossing to a parental plant and out-crossing with a non-transgenic plant are also contemplated, as is vegetative propagation. Descriptions of other breeding methods that are commonly used for different traits and crops can be found in one of several references, e.g., Fehr, in Breeding Methods for Cultivar Development, Wilcos J. ed., American Society of Agronomy, Madison Wis. (1987).
One particularly useful application of the claimed invention is to combine the high oleic acid trait of the DP-305423-1 event with other soybean lines that have altered fatty acid compositions to obtain progeny lines with novel fatty acid compositions and/or improved agronomic traits. The other soybean lines may be mutant lines, transgenic lines, or transgenic lines that also comprise a mutated gene. The transgenes of DP-305423-1 may be combined with mutant genes or other transgenes either by making a genetic cross or by transforming the other soybean line with the recombinant DNA constructs of the invention.
As examples, the high oleic acid trait of the invention can be combined with a mutant line having a high stearic acid phenotype, such as soybean line A6 [Hammond, E. G. and Fehr, W. R. (1983)] or with a mutant line having a low linolenic acid phenotype such as soybean mutant lines A5, A23, A16 and C1640 [Fehr, W. R. et al. (1992) in Crop Science 32:903-906]. Oils produced from such combinations would provide improved feedstocks for production of margarines, shortenings, spray coating and frying oils and would eliminate or reduce the need for hydrogenation. Furthermore, these oils would provide a health benefit for consumers, for example by reducing or eliminating trans fatty acids which have been found to be associated with high risk to cardiovascular diseases.
The high oleic acid trait of the invention also can be combined with mutant lines that have a high oleic acid phenotype. Examples of high oleic acid mutant lines include soybean lines A5 and N782245 [Martin, B. A. and Rinne, R. W. (1985) Crop Science 25:1055-1058].
As used herein, the use of the term “polynucleotide” is not intended to limit the present invention to polynucleotides comprising DNA. Those of ordinary skill in the art will recognize that polynucleotides, can comprise ribonucleotides and combinations of ribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues. The polynucleotides of the invention also encompass all forms of sequences including, but not limited to, single-stranded forms, double-stranded forms, hairpins, stem-and-loop structures, and the like.
A DP-305423-1 plant comprises a suppression cassette containing a 597 bp fragment of the soybean microsomal omega-6 desaturase gene 1 (gm-fad2-1) and an expression cassette containing a modified version of the soybean acetolactate synthase gene (gm-hra). The cassette can include 5′ and 3′ regulatory sequences operably linked to the gm-fad2-1 and the gm-hra polynucleotides. “Operably linked” is intended to mean a functional linkage between two or more elements. For example, an operable linkage between a polynucleotide of interest and a regulatory sequence (i.e., a promoter) is functional link that allows for the expression of the polynucleotide of interest. Operably linked elements may be contiguous or non-contiguous. When used to refer to the joining of two protein coding regions, by operably linked it is intended that the coding regions are in the same reading frame. The cassette may additionally contain at least one additional gene to be cotransformed into the organism. Alternatively, the additional gene(s) can be provided on multiple expression cassettes. Such an expression cassette is provided with a plurality of restriction sites and/or recombination sites for insertion of the polynucleotide to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain selectable marker genes.
The expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a coding region, and a transcriptional and translational termination region functional in plants. “Promoter” refers to a nucleotide sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3′ to a promoter sequence. The promoter sequence can comprise proximal and more distal upstream elements, the latter elements are often referred to as enhancers. Accordingly, an “enhancer” is a nucleotide sequence that can stimulate promoter activity and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue-specificity of a promoter. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic nucleotide segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. Promoters that cause a nucleic acid fragment to be expressed in most cell types at most times are commonly referred to as “constitutive promoters”. New promoters of various types useful in plant cells are constantly being discovered; numerous examples may be found in the compilation by Okamuro and Goldberg (1989) Biochemistry of Plants 15: 1-82. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, nucleic acid fragments of different lengths may have identical promoter activity.
The expression cassettes may also contain 5′ leader sequences. Such leader sequences can act to enhance translation. The regulatory regions (i.e., promoters, transcriptional regulatory regions, RNA processing or stability regions, introns, polyadenylation signals, and translational termination regions) and/or the coding region may be native/analogous or heterologous to the host cell or to each other.
The “translation leader sequence” refers to a nucleotide sequence located between the promoter sequence of a gene and the coding sequence. The translation leader sequence is present in the fully processed mRNA upstream of the translation start sequence. The translation leader sequence may affect numerous parameters including, processing of the primary transcript to mRNA, mRNA stability and/or translation efficiency. Examples of translation leader sequences have been described (Turner and Foster (1995) Mol. Biotechnol. 3: 225-236). The “3′ non-coding sequences” refer to nucleotide sequences located downstream of a coding sequence and include polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor. The use of different 3′ non-coding sequences is exemplified by Ingelbrecht et al. (1989) Plant Cell 1: 671-680.
As used herein, “heterologous” in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention. For example, a promoter operably linked to a heterologous polynucleotide is from a species different from the species from which the polynucleotide was derived, or, if from the same/analogous species, one or both are substantially modified from their original form and/or genomic locus, or the promoter is not the native promoter for the operably linked polynucleotide.
In preparing the expression cassette, the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved. The expression cassette can also comprise a selectable marker gene for the selection of transformed cells. Selectable marker genes are utilized for the selection of transformed cells or tissues.
Isolated polynucleotides are provided that can be used in various methods for the detection and/or identification of the soybean DP-305423-1 event. An “isolated” or “purified” polynucleotide, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polynucleotide as found in its naturally occurring environment. Thus, an isolated or purified polynucleotide is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. Optimally, an “isolated” polynucleotide is free of sequences (optimally protein encoding sequences) that naturally flank the polynucleotide (i.e., sequences located at the 5′ and 3′ ends of the polynucleotide) in the genomic DNA of the organism from which the polynucleotide is derived. For example, in various embodiments, the isolated polynucleotide can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequence that naturally flank the polynucleotide in genomic DNA of the cell from which the polynucleotide is derived.
In specific embodiments, the polynucleotides of the invention comprise the junction DNA sequence set forth in SEQ ID NO:8, 9, 14, 15, 20, 21, 83 or 84. In other embodiments, the polynucleotides of the invention comprise the junction DNA sequences set forth in SEQ ID NO:5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 82, 83, 84, 85, 86, 87 or 88 or variants and fragments thereof. Fragments and variants of junction DNA sequences are suitable for discriminatively identifying event DP-305423-1. As discussed elsewhere herein, such sequences find use as primer and/or probes.
Another embodiment is a DNA expression construct comprising the isolated polynucleotide of the invention operably linked to at least one regulatory sequence.
Another embodiment is a recombinant DNA construct comprising: a first and second expression cassette, wherein said first expression cassette in operable linkage comprises: (a) a soybean KTi3 promoter; (b) a gm-fad2-1 fragment; and (c) a soybean KTi3 transcriptional terminator; and said second expression cassette comprising in operable linkage: (i) a soybean SAMS promoter; (ii) a soybean SAMS 5′ untranslated leader and intron; (iii) a soybean gm-hra encoding DNA molecule; and (iv) a soybean als transcriptional terminator.
Another embodiment is a transgenic soybean plant having stably integrated into its genome the polynucleotide or the recombinant DNA construct of the invention, and transgenic seed and transgenic progeny drived from said transgenic soybean plant, each also comprising the polynucleotide or recombinant DNA construct of the invention.
In other embodiments, the polynucleotides of the invention comprise polynucleotides that can detect a DP-305423-1 event or a DP-305423-1 specific region. Such sequences include any polynucleotide set forth in SEQ ID NOS:1-90 or variants and fragments thereof. Fragments and variants of polynucleotides that detect a DP-305423-1 event or a DP-305423-1 specific region are suitable for discriminatively identifying event DP-305423-1. As discussed elsewhere herein, such sequences find us as primer and/or probes. Further provided are isolated DNA nucleotide primer sequences comprising or consisting of a sequence set forth in SEQ ID NO:26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 89, or 90, or a complement thereof.
“Variants” is intended to mean substantially similar sequences. For polynucleotides, a variant comprises a polynucleotide having deletions (i.e., truncations) at the 5′ and/or 3′ end; deletion and/or addition of one or more nucleotides at one or more internal sites in the native polynucleotide; and/or substitution of one or more nucleotides at one or more sites in the native polynucleotide.
As used herein, a “probe” is an isolated polynucleotide to which is attached a conventional detectable label or reporter molecule, e.g., a radioactive isotope, ligand, chemiluminescent agent, enzyme, etc. Such a probe is complementary to a strand of a target polynucleotide, in the case of the present invention, to a strand of isolated DNA from soybean event DP-305423-1 whether from a soybean plant or from a sample that includes DNA from the event. Probes according to the present invention include not only deoxyribonucleic or ribonucleic acids but also polyam ides and other probe materials that can specifically detect the presence of the target DNA sequence.
As used herein, “primers” are isolated polynucleotides that are annealed to a complementary target DNA strand by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand, then extended along the target DNA strand by a polymerase, e.g., a DNA polymerase. Primer pairs of the invention refer to their use for amplification of a target polynucleotide, e.g., by the polymerase chain reaction (PCR) or other conventional nucleic-acid amplification methods. “PCR” or “polymerase chain reaction” is a technique used for the amplification of specific DNA segments (see, U.S. Pat. Nos. 4,683,195 and 4,800,159; herein incorporated by reference). Any combination of primers disclosed herein can be used such that the pair allows for the detection a DP-305423-1 event or specific region. Non-limiting examples of primer pairs include SEQ ID NOS:26 and 27; SEQ ID NOS:29 and 30; SEQ ID NOS:31 and 32; SEQ ID NOS:33 AND 32; SEQ ID NOS:35 and 36; SEQ ID NOS:37 and 38; SEQ ID NOS:39 and 40; SEQ ID NO:41 and 42; SEQ ID NOS:43 and 44; SEQ ID NOS:45 and 46; SEQ ID NOS:47 and 48; SEQ ID NOS:47 and 49; SEQ ID NOS:50 and 51; SEQ ID NOS:52 and 53; SEQ ID NOS:54 and 49; SEQ ID NOS:55 and 46; SEQ ID NOS:33 and 56; SEQ ID NOS:57 and 58; SEQ ID NOS:59 and 60; SEQ ID NOS:61 and 36; SEQ ID NOS:35 and 62; SEQ ID NOS:37 and 63; SEQ ID NOS:64 and 65; SEQ ID NOS:66 and 67; SEQ ID NOS:68 and 69; SEQ ID NOS:70 and 71; SEQ ID NOS:72 and 73; SEQ ID NOS:74 and 75; SEQ ID NOS:76 and 77; SEQ ID NOS:78 and 79; SEQ ID NOS:80 and 81; and SEQ ID NOS:89 and 90.
Probes and primers are of sufficient nucleotide length to bind to the target DNA sequence and specifically detect and/or identify a polynucleotide having a DP-305423-1 event. It is recognized that the hybridization conditions or reaction conditions can be determined by the operator to achieve this result. This length may be of any length that is of sufficient length to be useful in a detection method of choice. Generally, 8, 11, 14, 16, 18, 20, 22, 24, 26, 28, 30, 40, 50, 75, 100, 200, 300, 400, 500, 600, 700 nucleotides or more, or between about 11-20, 20-30, 30-40, 40-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, or more nucleotides in length are used. Such probes and primers can hybridize specifically to a target sequence under high stringency hybridization conditions.
Probes and primers according to embodiments of the present invention may have complete DNA sequence identity of contiguous nucleotides with the target sequence, although probes differing from the target DNA sequence and that retain the ability to specifically detect and/or identify a target DNA sequence may be designed by conventional methods. Accordingly, probes and primers can share about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater sequence identity or complementarity to the target polynucleotide (i.e., SEQ ID NO:1-90), or can differ from the target sequence (i.e., SEQ ID NO:1-90) by 1, 2, 3, 4, 5, 6 or more nucleotides. Probes can be used as primers, but are generally designed to bind to the target DNA or RNA and are not used in an amplification process.
Specific primers can be used to amplify an integration fragment to produce an amplicon that can be used as a “specific probe” or can itself be detected for identifying event DP-305423-1 in biological samples. Alternatively, a probe of the invention can be used during the PCR reaction to allow for the detection of the amplification event (i.e., a taqman probe). When the probe is hybridized with the polynucleotides of a biological sample under conditions which allow for the binding of the probe to the sample, this binding can be detected and thus allow for an indication of the presence of event DP-305423-1 in the biological sample. Such identification of a bound probe has been described in the art. In an embodiment of the invention, the specific probe is a sequence which, under optimized conditions, hybridizes specifically to a region within the 5′ or 3′ flanking region of the event and also comprises a part of the foreign DNA contiguous therewith. The specific probe may comprise a sequence of at least 80%, between 80 and 85%, between 85 and 90%, between 90 and 95%, and between 95 and 100% identical (or complementary) to a specific region of the DP-305423-1 event.
As used herein, “amplified DNA” or “amplicon” refers to the product of polynucleotide amplification of a target polynucleotide that is part of a nucleic acid template. For example, to determine whether a soybean plant resulting from a sexual cross contains the DP-305423-1 event, DNA extracted from the soybean plant tissue sample may be subjected to a polynucleotide amplification method using a DNA primer pair that includes a first primer derived from flanking sequence adjacent to the insertion site of inserted heterologous DNA, and a second primer derived from the inserted heterologous DNA to produce an amplicon that is diagnostic for the presence of the DP-305423-1 event DNA. By “diagnostic” for a DP-305423-1 event the use of any method or assay which discriminates between the presence or the absence of a DP-305423-1 event in a biological sample is intended. Alternatively, the second primer may be derived from the flanking sequence. In still other embodiments, primer pairs can be derived from flanking sequence on both sides of the inserted DNA so as to produce an amplicon that includes the entire insert polynucleotide of the expression construct as well as the sequence flanking the transgenic insert. The amplicon is of a length and has a sequence that is also diagnostic for the event (i.e., has a junction DNA from a DP-305423-1 event). The amplicon may range in length from the combined length of the primer pairs plus one nucleotide base pair to any length of amplicon producible by a DNA amplification protocol. A member of a primer pair derived from the flanking sequence may be located a distance from the inserted DNA sequence, this distance can range from one nucleotide base pair up to the limits of the amplification reaction, or about twenty thousand nucleotide base pairs. The use of the term “amplicon” specifically excludes primer dimers that may be formed in the DNA thermal amplification reaction.
Methods for preparing and using probes and primers are described, for example, in Molecular Cloning: A Laboratory Manual, 2.sup.nd ed, vol. 1-3, ed. Sambrook et al., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. 1989 (hereinafter, “Sambrook et al., 1989”); Current Protocols in Molecular Biology, ed. Ausubel et al., Greene Publishing and Wiley-Interscience, New York, 1992 (with periodic updates) (hereinafter, “Ausubel et al., 1992”); and Innis et al., PCR Protocols: A Guide to Methods and Applications, Academic Press: San Diego, 1990. PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as the PCR primer analysis tool in Vector NTI version 6 (Informax Inc., Bethesda Md.); PrimerSelect (DNASTAR
Inc., Madison, Wis.); and Primer (Version 0.5.COPYRGT., 1991, Whitehead Institute for Biomedical Research, Cambridge, Mass.). Additionally, the sequence can be visually scanned and primers manually identified using guidelines known to one of skill in the art.
It is to be understood that as used herein the term “transgenic” includes any cell, cell line, callus, tissue, plant part, or plant, the genotype of which has been altered by the presence of a heterologous nucleic acid including those transgenics initially so altered as well as those created by sexual crosses or asexual propagation from the initial transgenic. The term “transgenic” as used herein does not encompass the alteration of the genome (chromosomal or extra-chromosomal) by conventional plant breeding methods or by naturally occurring events such as random cross-fertilization, non-recombinant viral infection, non-recombinant bacterial transformation, non-recombinant transposition, or spontaneous mutation.
“Transformation” refers to the transfer of a nucleic acid fragment into the genome of a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as “transgenic” organisms. Examples of methods of plant transformation include Agrobacterium-mediated transformation (De Blaere et al. (1987) Meth. Enzymol. 143: 277) and particle-accelerated or “gene gun” transformation technology (Klein et al. (1987) Nature (London) 327: 70-73; U.S. Pat. No. 4,945,050, incorporated herein by reference). Additional transformation methods are disclosed below.
Thus, isolated polynucleotides of the invention can be incorporated into recombinant constructs, typically DNA constructs, which are capable of introduction into and replication in a host cell. Such a construct can be a vector that includes a replication system and sequences that are capable of transcription and translation of a polypeptide-encoding sequence in a given host cell. A number of vectors suitable for stable transfection of plant cells or for the establishment of transgenic plants have been described in, e.g., Pouwels et al. (1985; Supp. 1987) Cloning Vectors: A Laboratory Manual, Weissbach and Weissbach (1989) Methods for Plant Molecular Biology (Academic Press, New York); and Flevin et al. (1990) Plant Molecular Biology Manual (Kluwer Academic Publishers). Typically, plant expression vectors include, for example, one or more cloned plant genes under the transcriptional control of 5′ and 3′ regulatory sequences and a dominant selectable marker. Such plant expression vectors also can contain a promoter regulatory region (e.g., a regulatory region controlling inducible or constitutive, environmentally- or developmentally-regulated, or cell- or tissue-specific expression), a transcription initiation start site, a ribosome binding site, an RNA processing signal, a transcription termination site, and/or a polyadenylation signal.
Various methods and compositions for identifying event DP-305423-1 are provided. Such methods find use in identifying and/or detecting a DP-305423-1 event in any biological material. Such methods include, for example, methods to confirm seed purity and methods for screening seeds in a seed lot for a DP-305423-1 event. In one embodiment, a method for identifying event DP-305423-1 in a biological sample is provided and comprises contacting the sample with a first and a second primer; and, amplifying a polynucleotide comprising a DP-305423-1 specific region.
A biological sample can comprise any sample in which one desires to determine if DNA having event DP-305423-1 is present. For example, a biological sample can comprise any plant material or material comprising or derived from a plant material such as, but not limited to, food or feed products. As used herein, “plant material” refers to material which is obtained or derived from a plant or plant part. In specific embodiments, the biological sample comprises a soybean tissue.
Primers and probes based on the flanking DNA and insert sequences disclosed herein can be used to confirm (and, if necessary, to correct) the disclosed sequences by conventional methods, e.g., by re-cloning and sequencing such sequences. The polynucleotide probes and primers of the present invention specifically detect a target DNA sequence. Any conventional nucleic acid hybridization or amplification method can be used to identify the presence of DNA from a transgenic event in a sample. By “specifically detect” it is intended that the polynucleotide can be used either as a primer to amplify a DP-305423-1 specific region or the polynucleotide can be used as a probe that hybridizes under stringent conditions to a polynucleotide having a DP-305423-1 event or a DP-305423-1 specific region. The level or degree of hybridization which allows for the specific detection of a DP-305423-1 event or a specific region of a DP-305423-1 event is sufficient to distinguish the polynucleotide with the DP-305423-1 specific region from a polynucleotide lacking this region and thereby allow for discriminately identifying a DP-305423-1 event. By “shares sufficient sequence identity or complentarity to allow for the amplification of a DP-305423-1 specific event” is intended the sequence shares at least 80%, 85%, 90%, 91%7 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identity or complementarity to a fragment or across the full length of the polynucleotide having the DP-305423-1 specific region.
Regarding the amplification of a target polynucleotide (e.g., by PCR) using a particular amplification primer pair, “stringent conditions” are conditions that permit the primer pair to hybridize to the target polynucleotide to which a primer having the corresponding wild-type sequence (or its complement) would bind and preferably to produce an identifiable amplification product (the amplicon) having a DP-305423-1 specific region in a DNA thermal amplification reaction. In a PCR approach, oligonucleotide primers can be designed for use in PCR reactions to amplify a DP-305423-1 specific region. Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). See also Innis et al., eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds. (1995) PCR Strategies (Academic Press, New York); and Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New York). Methods of amplification are further described in U.S. Pat. Nos. 4,683,195, 4,683,202 and Chen et al. (1994) PNAS 91:5695-5699. These methods as well as other methods known in the art of DNA amplification may be used in the practice of the embodiments of the present invention. It is understood that a number of parameters in a specific PCR protocol may need to be adjusted to specific laboratory conditions and may be slightly modified and yet allow for the collection of similar results. These adjustments will be apparent to a person skilled in the art.
The amplified polynucleotide (amplicon) can be of any length that allows for the detection of the DP-305423-1 event or a DP-305423-1 specific region. For example, the amplicon can be about 10, 50, 100, 200, 300, 500, 700, 100, 2000, 3000, 4000, 5000 nucleotides in length or longer.
In specific embodiments, the specific region of the DP-305423-1 event is detected.
Any primer can be employed in the methods of the invention that allows a DP-305423-1 specific region to be amplified and/or detected. For example, in specific embodiments, the first primer comprises a fragment of a polynucleotide of SEQ ID NO:5, 6, 7 or 82, wherein the first or the second primer shares sufficient sequence identity or complementarity to the polynucleotide to amplify the DP-305423-1 specific region. The primer pair can comprise a first primer that comprises a fragment of a 5′ genomic region of SEQ ID NO:5, 6, 7 or 82, and a second primer that comprises a fragment of a 3′ genomic region of SEQ ID NO:5, 6, 7 or 82, or an insert region of SEQ ID NO:5, 6, 7 or 82, or alternatively, the primer pair can comprise a first primer that comprises a fragment of a 3′ genomic region of SEQ ID NO:5, 6, 7 or 82, and a second primer that comprises a fragment of a 5′ genomic region of SEQ ID NO:5, 6, 7 or 82, or an insert region of SEQ ID NO:5, 6, 7 or 82. In still further embodiments, the first and the second primer can comprise any one or any combination of the sequences set forth in SEQ ID NO:26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 89, or 90. The primers can be of any length sufficient to amplify a DP-305423-1 region including, for example, at least 6, 7, 8, 9, 10, 15, 20, 15, or 30 or about 7-10, 10-15, 15-20, 20-25, 25-30, 30-35, 35-40, 40-45 nucleotides or longer.
As discussed elsewhere herein, any method to PCR amplify the DP-305423-1 event or specific region can be employed, including for example, real time PCR. See, for example, Livak et al. (1995a) Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system for detecting PCR product and nucleic acid hybridization. PCR methods and Applications. 4:357-362; U.S. Pat. No. 5,538,848; U.S. Pat. No. 5,723,591; Applied Biosystems User Bulletin No. 2, “Relative Quantitation of Gene Expression,” P/N 4303859; and, Applied Biosystems User Bulletin No. 5, “Multiplex PCR with Taqman VIC probes,” P/N 4306236; each of which is herein incorporated by reference.
Thus, in specific embodiments, a method of detecting the presence of soybean event DP-305423-1 or progeny thereof in a biological sample is provided. The method comprises (a) extracting a DNA sample from the biological sample; (b) providing a pair of DNA primer molecules, including, but not limited to, i) the sequences comprising SEQ ID NO:26 and SEQ ID NO:27; ii) the sequences comprising SEQ ID NO:29 and SEQ ID NO:30; iii) the sequences comprising SEQ ID NO:31 and SEQ ID NO:32; iv) the sequences comprising SEQ ID NO:33 and SEQ ID NO:32; v) the sequences comprising SEQ ID NO:35 and SEQ ID NO:36; vi) the sequences comprising SEQ ID NO:37 and SEQ ID NO:38; vii) the sequences comprising SEQ ID NO:39 and SEQ ID NO:40; viii) the sequences comprising SEQ ID NO:41 and SEQ ID NO:42; ix) the sequences comprising SEQ ID NO:43 and SEQ ID NO:44; x) the sequences comprising SEQ ID NO:45 and SEQ ID NO:46; xi) the sequences comprising SEQ ID NO:47 and SEQ ID NO:48; xii) the sequences comprising SEQ ID NO:47 and SEQ ID NO:49; xiii) the sequences comprising SEQ ID NO:50 and SEQ ID NO:51; xiv) the sequences comprising SEQ ID NO:52 and SEQ ID NO:53; xv) the sequences comprising SEQ ID NO:54 and SEQ ID NO:49; xvi) the sequences comprising SEQ ID NO:55 and SEQ ID NO:46; xvii) the sequences comprising SEQ ID NO:33 and SEQ ID NO:56; xviii) the sequences comprising SEQ ID NO:57 and SEQ ID NO:58; xix) the sequences comprising SEQ ID NO:59 and SEQ ID NO:60; xx) the sequences comprising SEQ ID NO:61 and SEQ ID NO:36; xxi) the sequences comprising SEQ ID NO:35 and SEQ ID NO:62; xxii) the sequences comprising SEQ ID NO:37 and SEQ ID NO:63; xxiii) the sequences comprising SEQ ID NO:64 and SEQ ID NO:65; xxiv) the sequences comprising SEQ ID NO:66 and SEQ ID NO:67; xxv) the sequences comprising SEQ ID NO:68 and SEQ ID NO:69; xxvi) the sequences comprising SEQ ID NO:70 and SEQ ID NO:71; xxvii) the sequences comprising SEQ ID NO:72 and SEQ ID NO:73; xxviii) the sequences comprising SEQ ID NO:74 and SEQ ID NO:75; xxix) the sequences comprising SEQ ID NO:76 and SEQ ID NO:77; xxx) the sequences comprising SEQ ID NO:78 and SEQ ID NO:79; xxxi) the sequences comprising SEQ ID NO:80 and SEQ ID NO:81; and xxxii) the sequences comprising SEQ ID NO:89 and SEQ ID NO:90 (c) providing DNA amplification reaction conditions; (d) performing the DNA amplification reaction, thereby producing a DNA amplicon molecule; and (e) detecting the DNA amplicon molecule, wherein the detection of said DNA amplicon molecule in the DNA amplification reaction indicates the presence of soybean event DP-305423-1. In order for a nucleic acid molecule to serve as a primer or probe it need only be sufficiently complementary in sequence to be able to form a stable double-stranded structure under the particular solvent and salt concentrations employed.
In hybridization techniques, all or part of a polynucleotide that selectively hybridizes to a target polynucleotide having a DP-305423-1 specific event is employed. By “stringent conditions” or “stringent hybridization conditions” when referring to a polynucleotide probe conditions under which a probe will hybridize to its target sequence to a detectably greater degree than to other sequences (e.g., at least 2-fold over background) are intended. Regarding the amplification of a target polynucleotide (e.g., by PCR) using a particular amplification primer pair, “stringent conditions” are conditions that permit the primer pair to hybridize to the target polynucleotide to which a primer having the corresponding wild-type. Stringent conditions are sequence-dependent and will be different in different circumstances. By controlling the stringency of the hybridization and/or washing conditions, target sequences that are 100% complementary to the probe can be identified (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of identity are detected (heterologous probing). Generally, a probe is less than about 1000 nucleotides in length or less than 500 nucleotides in length.
As used herein, a substantially identical or complementary sequence is a polynucleotide that will specifically hybridize to the complement of the nucleic acid molecule to which it is being compared under high stringency conditions. Appropriate stringency conditions which promote DNA hybridization, for example, 6× sodium chloride/sodium citrate (SSC) at about 45° C., followed by a wash of 2×SSC at 50° C., are known to those skilled in the art or can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. Typically, stringent conditions for hybridization and detection will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in 1× to 2× SSC (20× SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1× SSC at 55 to 60° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1× SSC at 60 to 65° C. Optionally, wash buffers may comprise about 0.1% to about 1% SDS. Duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours. The duration of the wash time will be at least a length of time sufficient to reach equilibrium.
In hybridization reactions, specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and Wahl (1984) Anal. Biochem. 138:267-284: Tm=81.5° C.+16.6 (log M)+0.41 (% GC)−0.61 (% form)−500/L; where M is the molarity of monovalent cations, % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. Tm is reduced by about 1° C. for each 1% of mismatching; thus, Tm, hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with ≥90% identity are sought, the Tm can be decreased 10° C. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C. lower than the thermal melting point (Tm); moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point (Tm); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the thermal melting point (Tm). Using the equation, hybridization and wash compositions, and desired Tm, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a Tm of less than 45° C. (aqueous solution) or 32° C. (formamide solution), it is optimal to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, New York); and Ausubel et al., eds. (1995) Current Protocols in Molecular Biology, Chapter 2 (Greene Publishing and Wiley-Interscience, New York). See Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.) and Haymes et al. (1985) In: Nucleic Acid Hybridization, a Practical Approach, IRL Press, Washington, D.C.
A polynucleotide is said to be the “complement” of another polynucleotide if they exhibit complementarity. As used herein, molecules are said to exhibit “complete complementarity” when every nucleotide of one of the polynucleotide molecules is complementary to a nucleotide of the other. Two molecules are said to be “minimally complementary” if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under at least conventional “low-stringency” conditions. Similarly, the molecules are said to be “complementary” if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under conventional “high-stringency” conditions.
Further provided are methods of detecting the presence of DNA corresponding to the DP-305423-1 event in a sample. In one embodiment, the method comprises (a) contacting the biological sample with a polynucleotide probe that hybridizes under stringent hybridization conditions with DNA from soybean event DP-305423-1 and specifically detects the DP-305423-1 event; (b) subjecting the sample and probe to stringent hybridization conditions; and (c) detecting hybridization of the probe to the DNA, wherein detection of hybridization indicates the presence of the DP-305423-1 event.
Various method can be used to detect the DP-305423-1 specific region or amplicon thereof, including, but not limited to, Genetic Bit Analysis (Nikiforov et al. (1994) Nucleic Acid Res. 22: 4167-4175) where a DNA oligonucleotide is designed which overlaps both the adjacent flanking DNA sequence and the inserted DNA sequence. The oligonucleotide is immobilized in wells of a microwell plate. Following PCR of the region of interest (using one primer in the inserted sequence and one in the adjacent flanking sequence) a single-stranded PCR product can be hybridized to the immobilized oligonucleotide and serve as a template for a single base extension reaction using a DNA polymerase and labeled ddNTPs specific for the expected next base. Readout may be fluorescent or ELISA-based. A signal indicates presence of the insert/flanking sequence due to successful amplification, hybridization, and single base extension.
Another detection method is the Pyrosequencing technique as described by Winge ((2000) Innov. Pharma. Tech. 00: 18-24). In this method, an oligonucleotide is designed that overlaps the adjacent DNA and insert DNA junction. The oligonucleotide is hybridized to a single-stranded PCR product from the region of interest (one primer in the inserted sequence and one in the flanking sequence) and incubated in the presence of a DNA polymerase, ATP, sulfurylase, luciferase, apyrase, adenosine 5′ phosphosulfate and luciferin. dNTPs are added individually and the incorporation results in a light signal which is measured. A light signal indicates the presence of the transgene insert/flanking sequence due to successful amplification, hybridization, and single or multi-base extension.
Fluorescence Polarization as described by Chen et al. ((1999) Genome Res. 9: 492-498, 1999) is also a method that can be used to detect an amplicon of the invention. Using this method, an oligonucleotide is designed which overlaps the flanking and inserted DNA junction. The oligonucleotide is hybridized to a single-stranded PCR product from the region of interest (one primer in the inserted DNA and one in the flanking DNA sequence) and incubated in the presence of a DNA polymerase and a fluorescent-labeled ddNTP. Single base extension results in incorporation of the ddNTP. Incorporation can be measured as a change in polarization using a fluorometer. A change in polarization indicates the presence of the transgene insert/flanking sequence due to successful amplification, hybridization, and single base extension.
Taqman® (PE Applied Biosystems, Foster City, Calif.) is described as a method of detecting and quantifying the presence of a DNA sequence and is fully understood in the instructions provided by the manufacturer. Briefly, a FRET oligonucleotide probe is designed which overlaps the flanking and insert DNA junction. The FRET probe and PCR primers (one primer in the insert DNA sequence and one in the flanking genomic sequence) are cycled in the presence of a thermostable polymerase and dNTPs. Hybridization of the FRET probe results in cleavage and release of the fluorescent moiety away from the quenching moiety on the FRET probe. A fluorescent signal indicates the presence of the flanking/transgene insert sequence due to successful amplification and hybridization.
Molecular Beacons have been described for use in sequence detection as described in Tyangi et al. ((1996) Nature Biotech. 14: 303-308). Briefly, a FRET oligonucleotide probe is designed that overlaps the flanking and insert DNA junction. The unique structure of the FRET probe results in it containing secondary structure that keeps the fluorescent and quenching moieties in close proximity. The FRET probe and PCR primers (one primer in the insert DNA sequence and one in the flanking sequence) are cycled in the presence of a thermostable polymerase and dNTPs. Following successful PCR amplification, hybridization of the FRET probe to the target sequence results in the removal of the probe secondary structure and spatial separation of the fluorescent and quenching moieties. A fluorescent signal results. A fluorescent signal indicates the presence of the flanking/transgene insert sequence due to successful amplification and hybridization.
A hybridization reaction using a probe specific to a sequence found within the amplicon is yet another method used to detect the amplicon produced by a PCR reaction.
As used herein, “kit” refers to a set of reagents for the purpose of performing the method embodiments of the invention, more particularly, the identification and/or the detection of the DP-305423-1 event in biological samples. The kit of the invention can be used, and its components can be specifically adjusted, for purposes of quality control (e.g. purity of seed lots), detection of event DP-305423-1 in plant material, or material comprising or derived from plant material, such as but not limited to food or feed products.
In specific embodiments, a kit for identifying event DP-305423-1 in a biological sample is provided. The kit comprises a first and a second primer, wherein the first and second primer amplify a polynucleotide comprising a DP-305423-1 specific region. In further embodiments, the kit also comprises a polynucleotide for the detection of the DP-305423-1 specific region. The kit can comprise, for example, a first primer comprising a fragment of a polynucleotide of SEQ ID NO:5, 6, 7 or 82, wherein the first or the second primer shares sufficient sequence homology or complementarity to the polynucleotide to amplify said DP-305423-1 specific region. For example, in specific embodiments, the first primer comprises a fragment of a polynucleotide of SEQ ID NO:5, 6, 7 or 82, wherein the first or the second primer shares sufficient sequence homology or complementarity to the polynucleotide to amplify said DP-305423-1 specific region. The primer pair can comprises a first primer that comprises a fragment of a 5′ genomic region of SEQ ID NO:5, 6, 7 or 82, and a second primer that comprises a fragment of a 3′ genomic region of SEQ ID NO:5, 6, 7 or 82, or an insert region of SEQ ID NO:5, 6, 7 or 82, or alternatively, the primer pair can comprise a first primer that comprises a fragment of a 3′ genomic region of SEQ ID NO:5, 6, 7 or 82, and a second primer that comprises a fragment of a 5′ genomic region of SEQ ID NO:5, 6, 7 or 82, or an insert region of SEQ ID NO:5, 6, 7 or 82. In still further embodiments, the first and the second primer can comprise any one or any combination of the sequences set forth in SEQ ID NO:26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 89, or 90. The primers can be of any length sufficient to amplify the DP-305423-1 region including, for example, at least 6, 7, 8, 9, 10, 15, 20, 15, or 30 or about 7-10, 10-15, 15-20, 20-25, 25-30, 30-35, 35-40, 40-45 nucleotides or longer.
Further provided are DNA detection kits comprising at least one polynucleotide that can specifically detect a DP-305423-1 specific region, wherein said polynucleotide comprises at least one DNA molecule of a sufficient length of contiguous nucleotides homologous or complementary to SEQ ID NO:5, 6, 7 or 82. In specific embodiments, the DNA detection kit comprises a polynucleotide having SEQ ID NO:8, 9, 14, 15, 20, 21, 83 or 84, or comprises a sequence which hybridizes with at least one sequence selected from the group consisting of: a) the sequences of a 5′ genomic region of SEQ ID NO:5, 6, 7 or 82, and the sequences of an insert region of SEQ ID NO:5, 6, 7 or 82; and, b) the sequences of a 3′ genomic region of SEQ ID NO:5, 6, 7 or 82, and the sequences of an insert region of SEQ ID NO:5, 6, 7 or 82.
Any of the polynucleotides and fragments and variants thereof employed in the methods and compositions of the invention can share sequence identity to a region of the transgene insert of the DP-305423-1 event, a junction sequence of the DP-305423-1 event or a flanking sequence of the DP-305423-1 event. Methods to determine the relationship of various sequences are known. As used herein, “reference sequence” is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence. As used herein, “comparison window” makes reference to a contiguous and specified segment of a polynucleotide sequence, wherein the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two polynucleotides. Generally, the comparison window is at least 20 contiguous nucleotides in length, and optionally can be 30, 40, 50, 100, or longer. Those of skill in the art understand that to avoid a high similarity to a reference sequence due to inclusion of gaps in the polynucleotide sequence a gap penalty is typically introduced and is subtracted from the number of matches.
Methods of alignment of sequences for comparison are well known in the art. Thus, the determination of percent sequence identity between any two sequences can be accomplished using a mathematical algorithm. Non-limiting examples of such mathematical algorithms are the algorithm of Myers and Miller (1988) CABIOS 4:11-17; the local alignment algorithm of Smith et al. (1981) Adv. Appl. Math. 2:482; the global alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453; the search-for-local alignment method of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. 85:2444-2448; the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 872264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877.
Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, Calif.); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the GCG Wisconsin Genetics Software Package, Version 10 (available from Accelrys Inc., 9685 Scranton Road, San Diego, Calif., USA). Alignments using these programs can be performed using the default parameters. The CLUSTAL program is well described by Higgins et al. (1988) Gene 73:237-244 (1988); Higgins et al. (1989) CABIOS 5:151-153; Corpet et al. (1988) Nucleic Acids Res. 16:10881-90; Huang et al. (1992) CABIOS 8:155-65; and Pearson et al. (1994) Meth. Mol. Biol. 24:307-331. The ALIGN program is based on the algorithm of Myers and Miller (1988) supra. A PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used with the ALIGN program when comparing amino acid sequences. The BLAST programs of Altschul et al (1990) J. Mol. Biol. 215:403 are based on the algorithm of Karlin and Altschul (1990) supra. BLAST nucleotide searches can be performed with the BLASTN program, score=100, wordlength=12, to obtain nucleotide sequences homologous to a nucleotide sequence encoding a protein of the invention. BLAST protein searches can be performed with the BLASTX program, score=50, wordlength=3, to obtain amino acid sequences homologous to a protein or polypeptide of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25:3389. Alternatively, PSI-BLAST (in BLAST 2.0) can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra. When utilizing BLAST, Gapped BLAST, PSI-BLAST, the default parameters of the respective programs (e.g., BLASTN for nucleotide sequences, BLASTX for proteins) can be used. See www.ncbi.nlm.nih.gov. Alignment may also be performed manually by inspection.
Sequence alignments and percent identity calculations may be determined using a variety of comparison methods designed to detect homologous sequences including, but not limited to, the Megalign® program of the LASERGENE® bioinformatics computing suite (DNASTAR® Inc., Madison, Wis.). For example, multiple alignment of the sequences provided herein can be performed using the Clustal V method of alignment (Higgins and Sharp (1989) CABIOS. 5:151-153) with the default parameters (GAP PENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwise alignments and calculation of percent identity of protein sequences using the Clustal V method are KTUPLE=1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5. For nucleic acids these parameters are KTUPLE=2, GAP PENALTY=5, WINDOW=4 and DIAGONALS SAVED=4. After alignment of the sequences, using the Clustal V program, it is possible to obtain “percent identity” and “divergence” values by viewing the “sequence distances” table on the same program.
Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity and % similarity for an amino acid sequence using GAP Weight of 8 and Length Weight of 2, and the BLOSUM62 scoring matrix; or any equivalent program thereof. By “equivalent program” any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10 is intended.
GAP uses the algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453, to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. GAP considers all possible alignments and gap positions and creates the alignment with the largest number of matched bases and the fewest gaps. It allows for the provision of a gap creation penalty and a gap extension penalty in units of matched bases. GAP must make a profit of gap creation penalty number of matches for each gap it inserts. If a gap extension penalty greater than zero is chosen, GAP must, in addition, make a profit for each gap inserted of the length of the gap times the gap extension penalty. Default gap creation penalty values and gap extension penalty values in Version 10 of the GCG Wisconsin Genetics Software Package for protein sequences are 8 and 2, respectively. For nucleotide sequences the default gap creation penalty is 50 while the default gap extension penalty is 3. The gap creation and gap extension penalties can be expressed as an integer selected from the group of integers consisting of from 0 to 200. Thus, for example, the gap creation and gap extension penalties can be 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65 or greater.
GAP presents one member of the family of best alignments. There may be many members of this family, but no other member has a better quality. GAP displays four figures of merit for alignments: Quality, Ratio, Identity, and Similarity. The Quality is the metric maximized in order to align the sequences. Ratio is the Quality divided by the number of bases in the shorter segment. Percent Identity is the percent of the symbols that actually match. Percent Similarity is the percent of the symbols that are similar. Symbols that are across from gaps are ignored. A similarity is scored when the scoring matrix value for a pair of symbols is greater than or equal to 0.50, the similarity threshold. The scoring matrix used in Version 10 of the GCG Wisconsin Genetics Software Package is BLOSUM62 (see Henikoff and Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915).
As used herein, “sequence identity” or “identity” in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. When sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences that differ by such conservative substitutions are said to have “sequence similarity” or “similarity”. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif.).
As used herein, “percentage of sequence identity” means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.
The present invention provides methods for controlling weeds in an area of cultivation, preventing the development or the appearance of herbicide resistant weeds in an area of cultivation, producing a crop, and increasing crop safety. The term “controlling,” and derivations thereof, for example, as in “controlling weeds” refers to one or more of inhibiting the growth, germination, reproduction, and/or proliferation of; and/or killing, removing, destroying, or otherwise diminishing the occurrence and/or activity of a weed.
As used herein, an “area of cultivation” comprises any region in which one desires to grow a plant. Such areas of cultivations include, but are not limited to, a field in which a plant is cultivated (such as a crop field, a sod field, a tree field, a managed forest, a field for culturing fruits and vegetables, etc), a greenhouse, a growth chamber, etc.
The methods of the invention comprise planting the area of cultivation with the soybean DP-305423-1 seeds or plants, and in specific embodiments, applying to the crop, seed, weed or area of cultivation thereof an effective amount of a herbicide of interest. It is recognized that the herbicide can be applied before or after the crop is planted in the area of cultivation. Such herbicide applications can include an application of an inhibitor of ALS. In specific embodiments, an inhibitor of ALS is applied to the soybean DP-305423-1 event, wherein the effective concentration of the ALS inhibitor would significantly damage an appropriate control plant. In one non-limiting embodiment, the herbicide comprises at least one of a sulfonylaminocarbonyltriazolinone; a triazolopyrimidine; a pyrimidinyl(thio)benzoate; an imidazolinone; a triazine; and/or a phosphinic acid.
In another non-limiting embodiment, the herbicide comprises imazapyr, chlorimuron-ethyl, quizalofop, or fomesafen, wherein an effective amount is tolerated by the crop and controls weeds. As disclosed elsewhere herein, any effective amount of these herbicides can be applied. In specific embodiments, an effective amount of imazapyr comprising about 7.5 to about 27.5 g ai/hectare; an effective amount of chlorimuron-ethyl comprising about 7.5 to about 27.5 g ai/hectare; an effective amount of quizalofop comprising about 50 to about 70 g ai/hectare; and, an effective amount of fomesafen comprising about 240 to about 260 g ai/hectare.
In other embodiments, a combination of at least two herbicides are applied. More details regarding the various herbicide combinations that can be employed in the methods of the invention are discussed elsewhere herein.
A “control” or “control plant” or “control plant cell” provides a reference point for measuring changes in phenotype of the subject plant or plant cell, and may be any suitable plant or plant cell. A control plant or plant cell may comprise, for example: (a) a wild-type plant or cell, i.e., of the same genotype as the starting material for the genetic alteration which resulted in the subject plant or cell; (b) a plant or plant cell of the same genotype as the starting material but which has been transformed with a null construct (i.e., with a construct which has no known effect on the trait of interest, such as a construct comprising a marker gene); (c) a plant or plant cell which is a non-transformed segregant among progeny of a subject plant or plant cell; (d) a plant or plant cell which is genetically identical to the subject plant or plant cell but which is not exposed to the same treatment (e.g., herbicide treatment) as the subject plant or plant cell; (e) the subject plant or plant cell itself, under conditions in which the gene of interest is not expressed; or (f) the subject plant or plant cell itself, under conditions in which it has not been exposed to a particular treatment such as, for example, a herbicide or combination of herbicides and/or other chemicals. In some instances, an appropriate control plant or control plant cell may have a different genotype from the subject plant or plant cell but may share the herbicide-sensitive characteristics of the starting material for the genetic alteration(s) which resulted in the subject plant or cell (see, e.g., Green (1998) Weed Technology 12: 474-477; Green and Ulrich (1993) Weed Science 41: 508-516. In some instances, an appropriate control soybean plant is a “Jack” soybean plant (Illinois Foundation Seed, Champaign, Ill.). In other embodiments, the null segregant can be used as a control, as they are genetically identical to DP-305423-1 with the exception of the transgenic insert DNA.
Any herbicide can be applied to the DP-305423-1 soybean crop, crop part, or the area of cultivation containing the crop plant. Classifications of herbicides (i.e., the grouping of herbicides into classes and subclasses) is well-known in the art and includes classifications by HRAC (Herbicide Resistance Action Committee) and WSSA (the Weed Science Society of America) (see also, Retzinger and Mallory-Smith (1997) Weed Technology 11: 384-393). An abbreviated version of the HRAC classification (with notes regarding the corresponding WSSA group) is set forth below in Table 2.
Herbicides can be classified by their mode of action and/or site of action and can also be classified by the time at which they are applied (e.g., preemergent or postemergent), by the method of application (e.g., foliar application or soil application), or by how they are taken up by or affect the plant. For example, thifensulfuron-methyl and tribenuron-methyl are applied to the foliage of a crop and are generally metabolized there, while rimsulfuron and chlorimuron-ethyl are generally taken up through both the roots and foliage of a plant. “Mode of action” generally refers to the metabolic or physiological process within the plant that the herbicide inhibits or otherwise impairs, whereas “site of action” generally refers to the physical location or biochemical site within the plant where the herbicide acts or directly interacts. Herbicides can be classified in various ways, including by mode of action and/or site of action (see, e.g., Table 2).
Often, a herbicide-tolerance gene that confers tolerance to a particular herbicide or other chemical on a plant expressing it will also confer tolerance to other herbicides or chemicals in the same class or subclass, for example, a class or subclass set forth in Table 2. Thus, in some embodiments of the invention, a transgenic plant of the invention is tolerant to more than one herbicide or chemical in the same class or subclass, such as, for example, an inhibitor of PPO, a sulfonylurea, or a synthetic auxin.
The invention provides a transgenic soybean plant which can be selected for use in crop production based on the prevalence of herbicide-tolerant weed species in the area where the transgenic crop is to be grown. Methods are known in the art for assessing the herbicide tolerance of various weed species. Weed management techniques are also known in the art, such as for example, crop rotation using a crop that is tolerant to a herbicide to which the local weed species are not tolerant. A number of entities monitor and publicly report the incidence and characteristics of herbicide-tolerant weeds, including the Herbicide Resistance Action Committee (HRAC), the Weed Science Society of America, and various state agencies (see, e.g., see, for example, herbicide tolerance scores for various broadleaf weeds from the 2004 Illinois Agricultural Pest Management Handbook), and one of skill in the art would be able to use this information to determine which crop and herbicide combinations should be used in a particular location.
These entities also publish advice and guidelines for preventing the development and/or appearance of and controlling the spread of herbicide tolerant weeds (see, e.g., Owen and Hartzler (2004), 2005 Herbicide Manual for Agricultural Professionals, Pub. WC 92 Revised (Iowa State University Extension, Iowa State University of Science and Technology, Ames, Iowa); Weed Control for Corn, Soybeans, and Sorghum, Chapter 2 of “2004 Illinois Agricultural Pest Management Handbook” (University of Illinois Extension, University of Illinois at Urbana-Champaign, Ill.); Weed Control Guide for Field Crops, MSU Extension Bulletin E434 (Michigan State University, East Lansing, Mich.)).
In one embodiment, one ALS inhibitor or at least two ALS inhibitors are applied to the DP-305423-1 soybean crop or area of cultivation. The ALS inhibitor can be applied at any effective rate that selectively controls weeds and does not significantly damage the crop. In specific embodiments, at least one ALS inhibitor is applied at a level that would significantly damage an appropriate control plant. In other embodiments, at least one ALS inhibitor is applied above the recommended label use rate for the crop. In still other embodiments, a mixture of ALS inhibitors is applied at a lower rate than the recommended use rate and weeds continue to be selectively controlled. Herbicides that inhibit acetolactate synthase (also known as acetohydroxy acid synthase) and are therefore useful in the methods of the invention include sulfonylureas as listed in Table 2, including agriculturally suitable salts (e.g., sodium salts) thereof; sulfonylaminocarbonyltriazolinones as listed in Table 2, including agriculturally suitable salts (e.g., sodium salts) thereof; triazolopyrimidines as listed in Table 2, including agriculturally suitable salts (e.g., sodium salts) thereof; pyrimidinyloxy(thio)benzoates as listed in Table 2, including agriculturally suitable salts (e.g., sodium salts) thereof; and imidazolinones as listed in Table 2, including agriculturally suitable salts (e.g., sodium salts) thereof. In some embodiments, methods of the invention comprise the use of a sulfonylurea which is not chlorimuron-ethyl, chlorsulfuron, rimsulfuron, thifensulfuron-methyl, or tribenuron-methyl.
Thus, in some embodiments, a transgenic plant of the invention is used in a method of growing a DP-305423-1 soybean crop by the application of herbicides to which the plant is tolerant. In this manner, treatment with a combination of one of more herbicides which include, but are not limited to: acetochlor, acifluorfen and its sodium salt, aclonifen, acrolein (2-propenal), alachlor, alloxydim, ametryn, am icarbazone, am idosulfuron, aminopyralid, am itrole, ammonium sulfamate, anilofos, asulam, atrazine, azimsulfuron, beflubutam id, benazolin, benazolin-ethyl, bencarbazone, benfluralin, benfuresate, bensulfuron-methyl, bensulide, bentazone, benzobicyclon, benzofenap, bifenox, bilanafos, bispyribac and its sodium salt, bromacil, bromobutide, bromofenoxim, bromoxynil, bromoxynil octanoate, butachlor, butafenacil, butamifos, butralin, butroxydim, butylate, cafenstrole, carbetamide, carfentrazone-ethyl, catechin, chlomethoxyfen, chloramben, chlorbromuron, chlorflurenol-methyl, chloridazon, chlorimuron-ethyl, chlorotoluron, chlorpropham, chlorsulfuron, chlorthal-dimethyl, chlorthiam id, cinidon-ethyl, cinmethylin, cinosulfuron, clethodim, clodinafop-propargyl, clomazone, clomeprop, clopyralid, clopyralid-olamine, cloransulam-methyl, CUH-35 (2-methoxyethyl 2-[[[4-chloro-2-fluoro-5-[(1-methyl-2-propynyl)oxy]phenyl](3-fluorobenzoyl)amino]carbonyl]-1-cyclohexene-1-carboxylate), cumyluron, cyanazine, cycloate, cyclosulfamuron, cycloxydim, cyhalofop-butyl, 2,4-D and its butotyl, butyl, isoctyl and isopropyl esters and its dimethylammonium, diolamine and trolamine salts, daimuron, dalapon, dalapon-sodium, dazomet, 2,4-DB and its dimethylammonium, potassium and sodium salts, desmedipham, desmetryn, dicamba and its diglycolammonium, dimethylammonium, potassium and sodium salts, dichlobenil, dichlorprop, diclofop-methyl, diclosulam, difenzoquat metilsulfate, diflufenican, diflufenzopyr, dimefuron, dimepiperate, dimethachlor, dimethametryn, dimethenam id, dimethenamid-P, dimethipin, dimethylarsinic acid and its sodium salt, dinitramine, dinoterb, diphenamid, diquat dibromide, dithiopyr, diuron, DNOC, endothal, EPTC, esprocarb, ethalfluralin, ethametsulfuron-methyl, ethofumesate, ethoxyfen, ethoxysulfuron, etobenzanid, fenoxaprop-ethyl, fenoxaprop-P-ethyl, fentrazamide, fenuron, fenuron-TCA, flamprop-methyl, flamprop-M-isopropyl, flamprop-M-methyl, flazasulfuron, florasulam, fluazifop-butyl, fluazifop-P-butyl, flucarbazone, flucetosulfuron, fluchloralin, flufenacet, flufenpyr, flufenpyr-ethyl, flumetsulam, flumiclorac-pentyl, flumioxazin, fluometuron, fluoroglycofen-ethyl, flupyrsulfuron-methyl and its sodium salt, flurenol, flurenol-butyl, fluridone, flurochloridone, fluroxypyr, flurtamone, fluthiacet-methyl, fomesafen, foramsulfuron, fosamine-ammonium, glufosinate, glufosinate-ammonium, glyphosate and its salts such as ammonium, isopropylammonium, potassium, sodium (including sesquisodium) and trimesium (alternatively named sulfosate), halosulfuron-methyl, haloxyfop-etotyl, haloxyfop-methyl, hexazinone, HOK-201 (N-(2,4-difluorophenyl)-1,5-dihydro-N-(1-methylethyl)-5-oxo-1-[(tetrahydro-2H-pyran-2-yl)methyl]-4H-1,2,4-triazole-4-carboxamide), imazamethabenz-methyl, imazamox, imazapic, imazapyr, imazaquin, imazaquin-ammonium, imazethapyr, imazethapyr-ammonium, imazosulfuron, indanofan, iodosulfuron-methyl, ioxynil, ioxynil octanoate, ioxynil-sodium, isoproturon, isouron, isoxaben, isoxaflutole, isoxachlortole, lactofen, lenacil, linuron, maleic hydrazide, MCPA and its salts (e.g., MCPA-dimethylammonium, MCPA-potassium and MCPA-sodium, esters (e.g., MCPA-2-ethylhexyl, MCPA-butotyl) and thioesters (e.g., MCPA-thioethyl), MCPB and its salts (e.g., MCPB-sodium) and esters (e.g., MCPB-ethyl), mecoprop, mecoprop-P, mefenacet, mefluidide, mesosulfuron-methyl, mesotrione, metam-sodium, metamifop, metamitron, metazachlor, methabenzthiazuron, methylarsonic acid and its calcium, monoammonium, monosodium and disodium salts, methyldymron, metobenzuron, metobromuron, metolachlor, S-metholachlor, metosulam, metoxuron, metribuzin, metsulfuron-methyl, molinate, monolinuron, naproanilide, napropamide, naptalam, neburon, nicosulfuron, norflurazon, orbencarb, oryzalin, oxadiargyl, oxadiazon, oxasulfuron, oxaziclomefone, oxyfluorfen, paraquat dichloride, pebulate, pelargonic acid, pendimethalin, penoxsulam, pentanochlor, pentoxazone, perfluidone, pethoxyam id, phenmedipham, picloram, picloram-potassium, picolinafen, pinoxaden, piperofos, pretilachlor, prim isulfuron-methyl, prodiamine, profoxydim, prometon, prometryn, propachlor, propanil, propaquizafop, propazine, propham, propisochlor, propoxycarbazone, propyzamide, prosulfocarb, prosulfuron, pyraclonil, pyraflufen-ethyl, pyrasulfotole, pyrazogyl, pyrazolynate, pyrazoxyfen, pyrazosulfuron-ethyl, pyribenzoxim, pyributicarb, pyridate, pyriftalid, pyriminobac-methyl, pyrimisulfan, pyrithiobac, pyrithiobac-sodium, pyroxsulam, quinclorac, quinmerac, quinoclamine, quizalofop-ethyl, quizalofop-P-ethyl, quizalofop-P-tefuryl, rimsulfuron, sethoxydim, siduron, simazine, simetryn, sulcotrione, sulfentrazone, sulfometuron-methyl, sulfosulfuron, 2,3,6-TBA, TCA, TCA-sodium, tebutam, tebuthiuron, tefuryltrione, tembotrione, tepraloxydim, terbacil, terbumeton, terbuthylazine, terbutryn, thenylchlor, thiazopyr, thiencarbazone, thifensulfuron-methyl, thiobencarb, tiocarbazil, topramezone, tralkoxydim, tri-allate, triasulfuron, triaziflam, tribenuron-methyl, triclopyr, triclopyr-butotyl, triclopyr-triethylammonium, tridiphane, trietazine, trifloxysulfuron, trifluralin, triflusulfuron-methyl, tritosulfuron and vernolate is disclosed.
Other suitable herbicides and agricultural chemicals are known in the art, such as, for example, those described in WO 2005/041654. Other herbicides also include bioherbicides such as Alternaria destruens Simmons, Colletotrichum gloeosporiodes (Penz.) Penz. & Sacc., Drechsiera monoceras (MTB-951), Myrothecium verrucaria (Albertini & Schweinitz) Ditmar: Fries, Phytophthora palmivora (Butl.) Butl. and Puccinia thlaspeos Schub. Combinations of various herbicides can result in a greater-than-additive (i.e., synergistic) effect on weeds and/or a less-than-additive effect (i.e. safening) on crops or other desirable plants. Herbicidally effective amounts of any particular herbicide can be easily determined by one skilled in the art through simple experimentation.
Herbicides may be classified into groups and/or subgroups as described herein above with reference to their mode of action, or they may be classified into groups and/or subgroups in accordance with their chemical structure.
Sulfonamide herbicides have as an essential molecular structure feature a sulfonamide moiety (—S(O)2NH—). As referred to herein, sulfonamide herbicides particularly comprise sulfonylurea herbicides, sulfonylaminocarbonyltriazolinone herbicides and triazolopyrimidine herbicides. In sulfonylurea herbicides the sulfonamide moiety is a component in a sulfonylurea bridge (—S(O)2NHC(O)NH(R)—). In sulfonylurea herbicides the sulfonyl end of the sulfonylurea bridge is connected either directly or by way of an oxygen atom or an optionally substituted amino or methylene group to a typically substituted cyclic or acyclic group. At the opposite end of the sulfonylurea bridge, the amino group, which may have a substituent such as methyl (R being CH3) instead of hydrogen, is connected to a heterocyclic group, typically a symmetric pyrimidine or triazine ring, having one or two substituents such as methyl, ethyl, trifluoromethyl, methoxy, ethoxy, methylamino, dimethylamino, ethylamino and the halogens. In sulfonylaminocarbonyltriazolinone herbicides, the sulfonamide moiety is a component of a sulfonylaminocarbonyl bridge (—S(O)2NHC(O)—). In sulfonylaminocarbonyltriazolinone herbicides the sulfonyl end of the sulfonylaminocarbonyl bridge is typically connected to substituted phenyl ring.
At the opposite end of the sulfonylaminocarbonyl bridge, the carbonyl is connected to the 1-position of a triazolinone ring, which is typically substituted with groups such as alkyl and alkoxy. In triazolopyrimidine herbicides the sulfonyl end of the sulfonamide moiety is connected to the 2-position of a substituted [1,2,4]triazolopyrimidine ring system and the amino end of the sulfonamide moiety is connected to a substituted aryl, typically phenyl, group or alternatively the amino end of the sulfonamide moiety is connected to the 2-position of a substituted [1,2,4]triazolopyrimidine ring system and the sulfonyl end of the sulfonamide moiety is connected to a substituted aryl, typically pyridinyl, group.
Representative of the sulfonylurea herbicides useful in the present invention are those of the formula:
wherein:
J is selected from the group consisting of
-
- J is R13SO2N(CH3)—;
- R is H or CH3;
- R1 is F, Cl, Br, NO2, C1-C4 alkyl, C1-C4 haloalkyl, C3-C4 cycloalkyl, C2-C4 haloalkenyl, C1-C4 alkoxy, C1-C4 haloalkoxy, C2-C4 alkoxyalkoxy, CO2R14, C(O)NR15R16, SO2NR17R18, S(O)nR19, C(O)R20, CH2CN or L;
- R2 is H, F, Cl, Br, I, CN, CH3, OCH3, SCH3, CF3 or OCF2H;
- R3 is Cl, NO2, CO2CH3, CO2CH2CH3, C(O)CH3, C(O)CH2CH3, C(O)-cyclopropyl, SO2N(CH3)2, SO2CH3, SO2CH2CH3, OCH3 or OCH2CH3;
- R4 is C1-C3 alkyl, C1-C2 haloalkyl, C1-C2 alkoxy, C2-C4 haloalkenyl, F, Cl, Br, NO2, CO2R14, C(O)NR15R16, SO2NR17R18, S(O)nR19, C(O)R20 or L;
- R5 is H, F, Cl, Br or CH3;
- R6 is C1-C3 alkyl optionally substituted with 0-3 F, 0-1 Cl and 0-1 C3-C4 alkoxyacetyloxy, or R6 is C1-C2 alkoxy, C2-C4 haloalkenyl, F, Cl, Br, CO2R14, C(O)NR15R16, SO2NR17R18, S(O)nR19, C(O)R20 or L;
- R7 is H, F, Cl, CH3 or CF3;
- R8 is H, C1-C3 alkyl or pyridinyl;
- R9 is C1-C3 alkyl, C1-C2 alkoxy, F, Cl, Br, NO2, CO2R14, SO2NR17R18, S(O)nR19, OCF2H, C(O)R20, C2-C4 haloalkenyl or L;
- R10 is H, Cl, F, Br, C1-C3 alkyl or C1-C2 alkoxy;
- R11 is H, C1-C3 alkyl, C1-C2 alkoxy, C2-C4 haloalkenyl, F, Cl, Br, CO2R14, C(O)NR15R16, SO2NR17R18, S(O)nR19, C(O)R20 or L;
- R12 is halogen, C1-C4 alkyl or C1-C3 alkylsulfonyl;
- R13 is C1-C4 alkyl;
- R14 is allyl, propargyl or oxetan-3-yl; or R14 is C1-C3 alkyl optionally substituted by at least one member independently selected from halogen, C1-C2 alkoxy and CN;
- R15 is H, C1-C3 alkyl or C1-C2 alkoxy;
- R16 is C1-C2 alkyl;
- R17 is H, C1-C3 alkyl, C1-C2 alkoxy, allyl or cyclopropyl;
- R18 is H or C1-C3 alkyl;
- R19 is C1-C3 alkyl, C1-C3 haloalkyl, allyl or propargyl;
- R20 is C1-C4 alkyl, C1-C4 haloalkyl or C3-C5 cycloalkyl optionally substituted by halogen;
- n is 0, 1 or 2;
- L is
-
- L1 is CH2, NH or O;
- R21 is H or C1-C3 alkyl;
- X is H, C1-C4 alkyl, C1-C4 alkoxy, C1-C4 haloalkoxy, C1-C4 haloalkyl, C1-C4 haloalkylthio, C1-C4 alkylthio, halogen, C2-C5 alkoxyalkyl, C2-C5 alkoxyalkoxy, amino, C1-C3 alkylamino or di(C1-C3 alkyl)amino;
- Y is H, C1-C4 alkyl, C1-C4 alkoxy, C1-C4 haloalkoxy, C1-C4 alkylthio, C1-C4 haloalkylthio, C2-C5 alkoxyalkyl, C2-C5 alkoxyalkoxy, amino, C1-C3 alkylamino, di(C1-C3 alkyl)amino, C3-C4 alkenyloxy, C3-C4 alkynyloxy, C2-C5 alkylthioalkyl, C2-C5 alkylsulfinylalkyl, C2-C5 alkylsulfonylalkyl, C1-C4 haloalkyl, C2-C4 alkynyl, C3-C5 cycloalkyl, azido or cyano; and
- Z is CH or N;
provided that (i) when one or both of X and Y is C1 haloalkoxy, then Z is CH; and (ii) when X is halogen, then Z is CH and Y is OCH3, OCH2CH3, N(OCH3)CH3, NHCH3, N(CH3)2 or OCF2H. Of note is the present single liquid herbicide composition comprising one or more sulfonylureas of Formula I wherein when R6 is alkyl, said alkyl is unsubstituted.
Representative of the triazolopyrimidine herbicides contemplated for use in this invention are those of the formula:
wherein:
-
- R22 and R23 each independently halogen, nitro, C1-C4 alkyl, C1-C4 haloalkyl, C1-C4 alkoxy, C1-C4 haloalkoxy or C2-C3 alkoxycarbonyl;
- R24 is H, halogen, C1-C2 alkyl or C1-C2 alkoxy;
- W is —NHS(O)2— or —S(O)2NH—;
- Y1 is H, C1-C2 alkyl or C1-C2 alkoxy;
- Y2 is H, F, Cl, Br, C1-C2 alkyl or C1-C2 alkoxy;
- Y3 is H, F or methoxy;
- Z1 is CH or N; and
- Z2 is CH or N;
provided that at least one of Y1 and Y2 is other than H.
In the above Markush description of representative triazolopyrimidine herbicides, when W is —NHS(O)2— the sulfonyl end of the sulfonamide moiety is connected to the [1,2,4]triazolopyrimidine ring system, and when W is —S(O)2NH— the amino end of the sulfonamide moiety is connected to the [1,2,4]triazolopyrimidine ring system.
In the above recitations, the term “alkyl”, used either alone or in compound words such as “alkylthio” or “haloalkyl” includes straight-chain or branched alkyl, such as, methyl, ethyl, n-propyl, i-propyl, or the different butyl isomers. “Cycloalkyl” includes, for example, cyclopropyl, cyclobutyl and cyclopentyl. “Alkenyl” includes straight-chain or branched alkenes such as ethenyl, 1-propenyl, 2-propenyl, and the different butenyl isomers. “Alkenyl” also includes polyenes such as 1,2-propadienyl and 2,4-butadienyl. “Alkynyl” includes straight-chain or branched alkynes such as ethynyl, 1-propynyl, 2-propynyl and the different butynyl isomers. “Alkynyl” can also include moieties comprised of multiple triple bonds such as 2,5-hexadiynyl. “Alkoxy” includes, for example, methoxy, ethoxy, n-propyloxy, isopropyloxy and the different butoxy isomers. “Alkoxyalkyl” denotes alkoxy substitution on alkyl. Examples of “alkoxyalkyl” include CH3OCH2, CH3OCH2CH2, CH3CH2OCH2, CH3CH2CH2CH2OCH2 and CH3CH2OCH2CH2. “Alkoxyalkoxy” denotes alkoxy substitution on alkoxy. “Alkenyloxy” includes straight-chain or branched alkenyloxy moieties. Examples of “alkenyloxy” include H2C═CHCH2O, (CH3)CH═CHCH2O and CH2═CHCH2CH2O. “Alkynyloxy” includes straight-chain or branched alkynyloxy moieties. Examples of “alkynyloxy” include HC≡CCH2O and CH3C≡CCH2O. “Alkylthio” includes branched or straight-chain alkylthio moieties such as methylthio, ethylthio, and the different propylthio isomers. “Alkylthioalkyl” denotes alkylthio substitution on alkyl. Examples of “alkylthioalkyl” include CH3SCH2, CH3SCH2CH2, CH3CH2SCH2, CH3CH2CH2CH2SCH2 and CH3CH2SCH2CH2; “alkylsulfinylalkyl” and “alkylsulfonylalkyl” include the corresponding sulfoxides and sulfones, respectively. Other substituents such as “alkylamino”, “dialkylamino” are defined analogously.
The total number of carbon atoms in a substituent group is indicated by the “Ci-Cj” prefix where i and j are numbers from 1 to 5. For example, C1-C4 alkyl designates methyl through butyl, including the various isomers. As further examples, C2 alkoxyalkyl designates CH3OCH2; C3 alkoxyalkyl designates, for example, CH3CH(OCH3), CH3OCH2CH2 or CH3CH2OCH2; and C4 alkoxyalkyl designates the various isomers of an alkyl group substituted with an alkoxy group containing a total of four carbon atoms, examples including CH3CH2CH2OCH2 and CH3CH2OCH2CH2.
The term “halogen”, either alone or in compound words such as “haloalkyl”, includes fluorine, chlorine, bromine or iodine. Further, when used in compound words such as “haloalkyl”, said alkyl may be partially or fully substituted with halogen atoms which may be the same or different. Examples of “haloalkyl” include F3C, CICH2, CF3CH2 and CF3CCl2. The terms “haloalkoxy”, “haloalkylthio”, and the like, are defined analogously to the term “haloalkyl”. Examples of “haloalkoxy” include CF3O, CCl3CH2O, HCF2CH2CH2O and CF3CH2O. Examples of “haloalkylthio” include CCl3S, CF3S, CCl3CH2S and CICH2CH2CH2S.
The following sulfonylurea herbicides illustrate the sulfonylureas useful for this invention: am idosulfuron (N-[[[[(4,6-dimethoxy-2-pyrimdinyl)amino]carbonyl]amino]-sulfonyl]-N-methylmethanesulfonamide), azimsulfuron (N-[[(4,6-dimethoxy-2-pyrimidinyl)amino]carbonyl]-1-methyl-4-(2-methyl-2H-tetrazol-5-yl)-1H-pyrazole-5-sulfonamimde), bensulfuron-methyl (methyl 2-[[[[[(4,6-dimethoxy-2-pyrimidinyl)amino]carbonyl]amino]sulfonyl]methyl]benzoate), chlorimuron-ethyl (ethyl 2-[[[[(4-chloro-6-methoxy-2-pyrimidinyl)amino]carbonyl]amino]sulfonyl]-benzoate), chlorsulfuron (2-chloro-N-[[(4-methoxy-6-methyl-1,3,5-triazin-2-yl)amino]-carbonyl]benzenesulfonamide), cinosulfuron (N-[[(4,6-dimethoxy-1,3,5-triazin-2-yl)amino]carbonyl]-2-(2-methoxyethoxy)benzenesulfonamide), cyclosulfamuron (N-[[[2-(cyclopropylcarbonyl)phenyl]amino]sulfonyl]-N1-(4,6-dimethoxypyrimidin-2-yl)urea), ethametsulfuron-methyl (methyl 2-[[[[[4-ethoxy-6-(methylamino)-1,3,5-triazin-2-yl]amino]carbonyl]amino]sulfonyl]benzoate), ethoxysulfuron (2-ethoxyphenyl [[(4,6-dimethoxy-2-pyrimidinyl)amino]carbonyl]sulfamate), flazasulfuron (N-[[(4,6-dimethoxy-2-pyrimidinyl)amino]carbonyl]-3-(trifluoromethyl)-2-pyridinesulfonamide), flucetosulfuron (1-[3-[[[[(4,6-dimethoxy-2-pyrimidinyl)-amino]carbonyl]amino]sulfonyl]-2-pyridinyl]-2-fluoropropyl methoxyacetate), flupyrsulfuron-methyl (methyl 2-[[[[(4,6-dimethoxy-2-pyrimidinyl)amino]carbonyl]-amino]sulfonyl]-6-(trifluoromethyl)-3-pyridinecarboxylate), foramsulfuron (2-[[[[(4,6-dimethoxy-2-pyrimidinyl)amino]carbonyl]amino]sulfonyl]-4-(formylamino)-N,N-dimethylbenzamide), halosulfuron-methyl (methyl 3-chloro-5-[[[[(4,6-dimethoxy-2-pyrimidinyl)amino]carbonyl]amino]sulfonyl]-1-methyl-1H-pyrazole-4-carboxylate), imazosulfuron (2-chloro-N-[[(4,6-dimethoxy-2-pyrimidinyl)amino]carbonyl]-imidazo[1,2-a]pyridine-3-sulfonamide), iodosulfuron-methyl (methyl 4-iodo-2-[[[[(4-methoxy-6-methyl-1,3,5-triazin-2-yl)amino]carbonyl]amino]sulfonyl]benzoate), mesosulfuron-methyl (methyl 2-[[[[(4,6-dimethoxy-2-pyrimidinyl)amino]carbonyl]-amino]sulfonyl]-4-[[(methylsulfonyl)amino]methyl]benzoate), metsulfuron-methyl (methyl 2-[[[[(4-methoxy-6-methyl-1,3,5-triazin-2-yl)amino]carbonyl]amino]sulfonyl]-benzoate), nicosulfuron (2-[[[[(4,6-dimethoxy-2-pyrimidinyl)amino]carbonyl]amino]-sulfonyl]-N,N-dimethyl-3-pyridinecarboxamide), oxasulfuron (3-oxetanyl 2-[[[[(4,6-dimethyl-2-pyrimidinyl)amino]carbonyl]amino]sulfonyl]benzoate), primisulfuron-methyl (methyl 2-[[[[[4,6-bis(trifluoromethoxy)-2-pyrimidinyl]amino]carbonyl]amino]sulfonyl]benzoate), prosulfuron (N-[[(4-methoxy-6-methyl-1,3,5-triazin-2-yl)amino]carbonyl]-2-(3,3,3-trifluoro-propyl)benzenesulfonamide), pyrazosulfuron-ethyl (ethyl 5-[[[[(4,6-dimethoxy-2-pyrimidinyl)amino]carbonyl]amino]sulfonyl]-1-methyl-1H-pyrazole-4-carboxylate), rimsulfuron (N-[[(4,6-dimethoxy-2-pyrimidinyl)amino]carbonyl]-3-(ethylsulfonyl)-2-pyridinesulfonamide), sulfometuron-methyl (methyl 2-[[[[(4,6-dimethyl-2-pyrimidinyl)amino]carbonyl]amino]sulfonyl]benzoate), sulfosulfuron (N-[[(4,6-dimethoxy-2-pyrimidinyl)amino]carbonyl]-2-(ethylsulfonyl)imidazo[1,2-a]pyridine-3-sulfonamide), thifensulfuron-methyl (methyl 3-[[[[(4-methoxy-6-methyl-1,3,5-triazin-2-yl)amino]carbonyl]amino]sulfonyl]-2-thiophenecarboxylate), triasulfuron (2-(2-chloroethoxy)-N-[[(4-methoxy-6-methyl-1,3,5-triazin-2-yl)amino]carbonyl]benzenesulfonamide), tribenuron-methyl (methyl 2-[[[[N-(4-methoxy-6-methyl-1,3,5-triazin-2-yl)-N-methylamino]carbonyl]amino]-sulfonyl]benzoate), trifloxysulfuron (N-[[(4,6-dimethoxy-2-pyrimidinyl)amino]-carbonyl]-3-(2,2,2-trifluoroethoxy)-2-pyridinesulfonamide), triflusulfuron-methyl (methyl 2-[[[[[4-dimethylamino)-6-(2,2,2-trifluoroethoxy)-1,3,5-triazin-2-yl]amino]-carbonyl]amino]sulfonyl]-3-methylbenzoate) and tritosulfuron (N-[[[4-methoxy-6-(trifluoromethyl)-1,3,5-triazin-2-yl]amino]carbonyl]-2-(trifluoromethyl)benzene-sulfonamide).
The following triazolopyrimidine herbicides illustrate the triazolopyrimidines useful for this invention: cloransulam-methyl (methyl 3-chloro-2-[[(5-ethoxy-7-fluoro-[1,2,4]triazolo[1,5-c]pyrimidin-2-yl)sulfonyl]amino]benzoate, diclosulam (N-(2,6-dichlorophenyl)-5-ethoxy-7-fluoro[1,2,4]triazolo[1,5-c]pyrimidine-2-sulfonamide, florasulam (N-(2,6-difluorophenyl)-8-fluoro-5-methoxy[1,2,4]triazolo[1,5-c]pyrimidine-2-sulfonamide), flumetsulam (N-(2,6-difluorophenyl)-5-methyl[1,2,4]triazolo[1,5-a]pyrimidine-2-sulfonamide), metosulam (N-(2,6-dichloro-3-methylphenyl)-5,7-dimethoxy[1,2,4]triazolo[1,5-a]pyrimidine-2-sulfonamide), penoxsulam (2-(2,2-difluoroethoxy)-N-(5,8-dimethoxy[1,2,4]triazolo[1,5-c]pyrimidin-2-yl)-6-(trifluoromethyl)benzenesulfonamide) and pyroxsulam (N-(5,7-dimethoxy[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)-2-methoxy-4-(trifluoromethyl)-3-pyridinesulfonamide).
The following sulfonylaminocarbonyltriazolinone herbicides illustrate the sulfonylaminocarbonyltriazolinones useful for this invention: flucarbazone (4,5-dihydro-3-methoxy-4-m ethyl-5-oxo-N-[[2-(trifluoromethoxy)phenyl]sulfonyl]-1H-1,2,4-triazole-1-carboxamide) and procarbazone (methyl 2-[[[(4,5-dihydro-4-methyl-5-oxo-3-propoxy-1H-1,2,4-triazol-1-yl)carbonyl]amino]sulfonyl]benzoate).
Additional herbicides include phenmedipham, triazolinones, and the herbicides disclosed in WO2006/012981, herein incorporated by reference in its entirety.
The methods further comprise applying to the crop and the weeds in a field a sufficient amount of at least one herbicide to which the crop seeds or plants is tolerant, such as, for example, glyphosate, a hydroxyphenylpyruvatedioxygenase inhibitor (e.g., mesotrione or sulcotrione), a phytoene desaturase inhibitor (e.g., diflufenican), a pigment synthesis inhibitor, sulfonamide, imidazolinone, bialaphos, phosphinothricin, azafenidin, butafenacil, sulfosate, glufosinate, triazolopyrimidine, pyrimidinyloxy(thio)benzoate, or sulonylaminocarbonyltriazolinone, an acetyl Co-A carboxylase inhibitor such as quizalofop-P-ethyl, a synthetic auxin such as quinclorac, or a protox inhibitor to control the weeds without significantly damaging the crop plants.
Generally, the effective amount of herbicide applied to the field is sufficient to selectively control the weeds without significantly affecting the crop. “Weed” as used herein refers to a plant which is not desirable in a particular area. Conversely, a “crop plant” as used herein refers to a plant which is desired in a particular area, such as, for example, a soybean plant. Thus, in some embodiments, a weed is a non-crop plant or a non-crop species, while in some embodiments, a weed is a crop species which is sought to be eliminated from a particular area, such as, for example, an inferior and/or non-transgenic soybean plant in a field planted with soybean event DP-305423-1, or a maize plant in a field planted with DP-305423-1. Weeds can be either classified into two major groups: monocots and dicots.
Many plant species can be controlled (i.e., killed or damaged) by the herbicides described herein. Accordingly, the methods of the invention are useful in controlling these plant species where they are undesirable (i.e., where they are weeds). These plant species include crop plants as well as species commonly considered weeds, including but not limited to species such as: blackgrass (Alopecurus myosuroides), giant foxtail (Setaria faberi), large crabgrass (Digitaria sanguinalis), Surinam grass (Brachiaria decumbens), wild oat (Avena fatua), common cocklebur (Xanthium pensylvanicum), common lam bsquarters (Chenopodium album), morning glory (Ipomoea coccinea), pigweed (Amaranthus spp.), velvetleaf (Abutilion theophrasti), common barnyardgrass (Echinochloa crus-galli), bermudagrass (Cynodon dactylon), downy brome (Bromus tectorum), goosegrass (Eleusine indica), green foxtail (Setaria viridis), Italian ryegrass (Lolium multiflorum), Johnsongrass (Sorghum halepense), lesser canarygrass (Phalaris minor), windgrass (Apera spica-venti), wooly cupgrass (Erichloa villosa), yellow nutsedge (Cyperus esculentus), common chickweed (Stellaria media), common ragweed (Ambrosia artemisiifolia), Kochia scoparia, horseweed (Conyza canadensis), rigid ryegrass (Lolium rigidum), goosegrass (Eleucine indica), hairy fleabane (Conyza bonariensis), buckhorn plantain (Plantago lanceolata), tropical spiderwort (Commelina benghalensis), field bindweed (Convolvulus arvensis), purple nutsedge (Cyperus rotundus), redvine (Brunnichia ovata), hemp sesbania (Sesbania exaltata), sicklepod (Senna obtusifolia), Texas blueweed (Helianthus ciliaris), and Devil's claws (Proboscidea louisianica). In other embodiments, the weed comprises a herbicide-resistant ryegrass, for example, a glyphosate resistant ryegrass, a paraquat resistant ryegrass, a ACCase-inhibitor resistant ryegrass, and a non-selective herbicide resistant ryegrass. In some embodiments, the undesired plants are proximate the crop plants.
As used herein, by “selectively controlled” it is intended that the majority of weeds in an area of cultivation are significantly damaged or killed, while if crop plants are also present in the field, the majority of the crop plants are not significantly damaged. Thus, a method is considered to selectively control weeds when at least 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or more of the weeds are significantly damaged or killed, while if crop plants are also present in the field, less than 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10, 5%, or 1% of the crop plants are significantly damaged or killed.
In some embodiments, a soybean DP-305423-1 plant of the invention is not significantly damaged by treatment with a particular herbicide applied to that plant at a dose equivalent to a rate of at least 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 150, 170, 200, 300, 400, 500, 600, 700, 800, 800, 1000, 2000, 3000, 4000, 5000 or more grams or ounces (1 ounce=29.57 ml) of active ingredient or commercial product or herbicide formulation per acre or per hectare, whereas an appropriate control plant is significantly damaged by the same treatment.
In specific embodiments, an effective amount of an ALS inhibitor herbicide comprises at least about 0.1, 1, 5, 10, 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 750, 800, 850, 900, 950, 1000, 2000, 3000, 4000, 5000, or more grams or ounces (1 ounce=29.57 ml) of active ingredient per hectare. In other embodiments, an effective amount of an ALS inhibitor comprises at least about 0.1-50, about 25-75, about 50-100, about 100-110, about 110-120, about 120-130, about 130-140, about 140-150, about 150-200, about 200-500, about 500-600, about 600-800, about 800-1000, or greater grams or ounces (1 ounce=29.57 ml) of active ingredient per hectare. Any ALS inhibitor, for example, those listed in Table 2 can be applied at these levels.
In other embodiments, an effective amount of a sulfonylurea comprises at least 0.1, 1, 5, 10, 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 5000 or more grams or ounces (1 ounce=29.57 ml) of active ingredient per hectare. In other embodiments, an effective amount of a sulfonylurea comprises at least about 0.1-50, about 25-75, about 50-100, about 100-110, about 110-120, about 120-130, about 130-140, about 140-150, about 150-160, about 160-170, about 170-180, about 190-200, about 200-250, about 250-300, about 300-350, about 350-400, about 400-450, about 450-500, about 500-550, about 550-600, about 600-650, about 650-700, about 700-800, about 800-900, about 900-1000, about 1000-2000, or more grams or ounces (1 ounce=29.57 ml) of active ingredient per hectare. Representative sulfonylureas that can be applied at this level are set forth in Table 2.
In other embodiments, an effective amount of a sulfonylaminocarbonyltriazolinones, triazolopyrimidines, pyrimidinyloxy(thio)benzoates, and imidazolinones can comprise at least about 0.1, 1, 5, 10, 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1500, 1550, 1600, 1650, 1700, 1800, 1850, 1900, 1950, 2000, 2500, 3500, 4000, 4500, 5000 or greater grams or ounces (1 ounce=29.57 ml) active ingredient per hectare. In other embodiments, an effective amount of a sulfonyluminocarbonyltriazolines, triazolopyrimidines, pyrimidinyloxy(thio)benzoates, or imidazolinones comprises at least about 0.1-50, about 25-75, about 50-100, about 100-110, about 110-120, about 120-130, about 130-140, about 140-150, about 150-160, about 160-170, about 170-180, about 190-200, about 200-250, about 250-300, about 300-350, about 350-400, about 400-450, about 450-500, about 500-550, about 550-600, about 600-650, about 650-700, about 700-800, about 800-900, about 900-1000, about 1000-2000, or more grams or ounces (1 ounce=29.57 ml) active ingredient per hectare.
Additional ranges of the effective amounts of herbicides can be found, for example, in various publications from University Extension services. See, for example, Bernards et al. (2006) Guide for Weed Management in Nebraska (www.ianrpubs.url.edu/sendlt/ec130); Regher et al. (2005) Chemical Weed Control for Fields Crops, Pastures, Rangeland, and Noncropland, Kansas State University Agricultural Extension Station and Corporate Extension Service; Zollinger et al. (2006) North Dakota Weed Control Guide, North Dakota Extension Service, and the Iowa State University Extension at www.weeds.iastate.edu, each of which is herein incorporated by reference.
Herbicides known to inhibit ALS vary in their active ingredient as well as their chemical formulations. One of skill in the art is familiar with the determination of the amount of active ingredient and/or acid equivalent present in a particular volume and/or weight of herbicide preparation.
Rates at which the ALS inhibitor herbicide is applied to the crop, crop part, seed or area of cultivation can be any of the rates disclosed herein. In specific embodiments, the rate for the ALS inhibitor herbicide is about 0.1 to about 5000 g ai/hectare, about 0.5 to about 300 g ai/hectare, or about 1 to about 150 g ai/hectare.
Generally, a particular herbicide is applied to a particular field (and any plants growing in it) no more than 1, 2, 3, 4, 5, 6, 7, or 8 times a year, or no more than 1, 2, 3, 4, or 5 times per growing season.
By “treated with a combination of” or “applying a combination of” herbicides to a crop, area of cultivation or field” it is intended that a particular field, crop or weed is treated with each of the herbicides and/or chemicals indicated to be part of the combination so that a desired effect is achieved, i.e., so that weeds are selectively controlled while the crop is not significantly damaged. In some embodiments, weeds which are susceptible to each of the herbicides exhibit damage from treatment with each of the herbicides which is additive or synergistic. The application of each herbicide and/or chemical may be simultaneous or the applications may be at different times, so long as the desired effect is achieved. Furthermore, the application can occur prior to the planting of the crop.
The proportions of herbicides used in the methods of the invention with other herbicidal active ingredients in herbicidal compositions are generally in the ratio of 5000:1 to 1:5000, 1000:1 to 1:1000, 100:1 to 1:100, 10:1 to 1:10 or 5:1 to 1:5 by weight. The optimum ratios can be easily determined by those skilled in the art based on the weed control spectrum desired. Moreover, any combinations of ranges of the various herbicides disclosed in Table 2 can also be applied in the methods of the invention.
Thus, in some embodiments, the invention provides improved methods for selectively controlling weeds in a field wherein the total herbicide application may be less than 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, 5%, or 1% of that used in other methods. Similarly, in some embodiments, the amount of a particular herbicide used for selectively controlling weeds in a field may be less than 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, 5%, or 1% of the amount of that particular herbicide that would be used in other methods, i.e., methods not utilizing a plant of the invention.
As used herein, the terms “synergy,” “synergistic,” “synergistically” and derivations thereof, such as in a “synergistic effect” or a “synergistic herbicide combination” or a “synergistic herbicide composition” refer to circumstances under which the biological activity of a combination of herbicides, such as at least a first herbicide and a second herbicide, is greater than the sum of the biological activities of the individual herbicides. Synergy, expressed in terms of a “Synergy Index (SI),” generally can be determined by the method described by Kull et al. Applied Microbiology 9, 538 (1961). See also Colby “Calculating Synergistic and Antagonistic Responses of Herbicide Combinations,” Weeds 15, 20-22 (1967).
In the same manner, in some embodiments, a DP-305423-1 soybean plant of the invention shows improved tolerance to a particular formulation of a herbicide active ingredient in comparison to an appropriate control plant. Herbicides are sold commercially as formulations which typically include other ingredients in addition to the herbicide active ingredient; these ingredients are often intended to enhance the efficacy of the active ingredient. Such other ingredients can include, for example, safeners and adjuvants (see, e.g., Green and Foy (2003) “Adjuvants: Tools for Enhancing Herbicide Performance,” in Weed Biology and Management, ed. Inderjit (Kluwer Academic Publishers, The Netherlands)). Thus, a DP-305423-1 soybean plant of the invention can show tolerance to a particular formulation of a herbicide (e.g., a particular commercially available herbicide product) that is at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12%, 15%, 17%, 20%, 22%, 25%, 27%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 80%, 90%, 100%, 125%, 150%, 175%, 200%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, 1000%, 1100%, 1200%, 1300%, 1400%, 1500%, 1600%, 1700%, 1800%, 1900%, or 2000% or more higher than the tolerance of an appropriate control plant that contains only a single herbicide tolerance gene which confers tolerance to the same herbicide formulation.
In other methods, a herbicide combination is applied over a DP-305423-1 soybean plant, where the herbicide combination produces either an additive or a synergistic effect for controlling weeds. Such combinations of herbicides can allow the application rate to be reduced, a broader spectrum of undesired vegetation to be controlled, improved control of the undesired vegetation with fewer applications, more rapid onset of the herbicidal activity, or more prolonged herbicidal activity.
An “additive herbicidal composition” has a herbicidal activity that is about equal to the observed activities of the individual components. A “synergistic herbicidal combination” has a herbicidal activity higher than what can be expected based on the observed activities of the individual components when used alone. Accordingly, the presently disclosed subject matter provides a synergistic herbicide combination, wherein the degree of weed control of the mixture exceeds the sum of control of the individual herbicides. In some embodiments, the degree of weed control of the mixture exceeds the sum of control of the individual herbicides by any statistically significant amount including, for example, about 1% to 5%, about 5% to about 10%, about 10% to about 20%, about 20% to about 30%, about 30% to 40%, about 40% to about 50%, about 50% to about 60%, about 60% to about 70%, about 70% to about 80%, about 80% to about 90%, about 90% to about 100%, about 100% to 120% or greater. Further, a “synergistically effective amount” of a herbicide refers to the amount of one herbicide necessary to elicit a synergistic effect in another herbicide present in the herbicide composition. Thus, the term “synergist,” and derivations thereof, refer to a substance that enhances the activity of an active ingredient (ai), i.e., a substance in a formulation from which a biological effect is obtained, for example, a herbicide.
Plants of the current invention can be crossed with transgenic plants that are tolerant to glyphosate, to produce progeny that have tolerance to both glyphosate and inhibitors of ALS.
Weeds that can be difficult to control with glyphosate alone in fields where a crop is grown (such as, for example, a soybean crop) include but are not limited to the following: horseweed (e.g., Conyza canadensis); rigid ryegrass (e.g., Lolium rigidum); goosegrass (e.g., Eleusine indica); Italian ryegrass (e.g., Lolium multiflorum); hairy fleabane (e.g., Conyza bonariensis); buckhorn plantain (e.g., Plantago lanceolata); common ragweed (e.g., Ambrosia artemisifolia); morning glory (e.g., Ipomoea spp.); waterhemp (e.g., Amaranthus spp.); field bindweed (e.g., Convolvulus arvensis); yellow nutsedge (e.g., Cyperus esculentus); common lambsquarters (e.g., Chenopodium album); wild buckwheat (e.g., Polygonium convolvulus); velvetleaf (e.g., Abutilon theophrasti); kochia (e.g., Kochia scoparia); and Asiatic dayflower (e.g., Commelina spp.). In areas where such weeds are found, the DP-305423-1 soybeans are particularly useful in allowing the treatment of a field (and therefore any crop growing in the field) with combinations of herbicides that would cause unacceptable damage to crop plants that did not contain both of these polynucleotides. Plants of the invention that are tolerant to glyphosate and other herbicides such as, for example, sulfonylurea, imidazolinone, triazolopyrimidine, pyrimidinyl(thio)benzoate, and/or sulfonylaminocarbonyltriazolinone herbicides in addition to being tolerant to at least one other herbicide with a different mode of action or site of action are particularly useful in situations where weeds are tolerant to at least two of the same herbicides to which the plants are tolerant. In this manner, plants of the invention make possible improved control of weeds that are tolerant to more than one herbicide.
In the methods of the invention, a herbicide may be formulated and applied to an area of interest such as, for example, a field or area of cultivation, in any suitable manner. A herbicide may be applied to a field in any form, such as, for example, in a liquid spray or as solid powder or granules. In specific embodiments, the herbicide or combination of herbicides that are employed in the methods comprise a tankmix or a premix. A herbicide may also be formulated, for example, as a “homogenous granule blend” produced using blends technology (see, e.g., U.S. Pat. No. 6,022,552, entitled “Uniform Mixtures of Pesticide Granules”). The blends technology of U.S. Pat. No. 6,022,552 produces a nonsegregating blend (i.e., a “homogenous granule blend”) of formulated crop protection chemicals in a dry granule form that enables delivery of customized mixtures designed to solve specific problems. A homogenous granule blend can be shipped, handled, subsampled, and applied in the same manner as traditional premix products where multiple active ingredients are formulated into the same granule.
Briefly, a “homogenous granule blend” is prepared by mixing together at least two extruded formulated granule products. In some embodiments, each granule product comprises a registered formulation containing a single active ingredient which is, for example, a herbicide, a fungicide, and/or an insecticide. The uniformity (homogeneity) of a “homogenous granule blend” can be optimized by controlling the relative sizes and size distributions of the granules used in the blend. The diameter of extruded granules is controlled by the size of the holes in the extruder die, and a centrifugal sifting process may be used to obtain a population of extruded granules with a desired length distribution (see, e.g., U.S. Pat. No. 6,270,025).
A homogenous granule blend is considered to be “homogenous” when it can be subsam pled into appropriately sized aliquots and the composition of each aliquot will meet the required assay specifications. To demonstrate homogeneity, a large sample of the homogenous granule blend is prepared and is then subsam pled into aliquots of greater than the minimum statistical sample size.
Blends also afford the ability to add other agrochemicals at normal, labeled use rates such as additional herbicides (a 3rd/4th mechanism of action), fungicides, insecticides, plant growth regulators and the like thereby saving costs associated with additional applications.
Any herbicide formulation applied over the DP-305423-1 soybean plant can be prepared as a “tank-mix” composition. In such embodiments, each ingredient or a combination of ingredients can be stored separately from one another. The ingredients can then be mixed with one another prior to application. Typically, such mixing occurs shortly before application. In a tank-mix process, each ingredient, before mixing, typically is present in water or a suitable organic solvent. For additional guidance regarding the art of formulation, see T. S. Woods, “The Formulator's Toolbox—Product Forms for Modern Agriculture” Pesticide Chemistry and Bioscience, The Food-Environment Challenge, T. Brooks and T. R. Roberts, Eds., Proceedings of the 9th International Congress on Pesticide Chemistry, The Royal Society of Chemistry, Cambridge, 1999, pp. 120-133. See also U.S. Pat. No. 3,235,361, Col. 6, line 16 through Col. 7, line 19 and Examples 10-41; U.S. Pat. No. 3,309,192, Col. 5, line 43 through Col. 7, line 62 and Examples 8, 12, 15, 39, 41, 52, 53, 58, 132, 138-140, 162-164, 166, 167 and 169-182; U.S. Pat. No. 2,891,855, Col. 3, line 66 through Col. 5, line 17 and Examples 1-4; Klingman, Weed Control as a Science, John Wiley and Sons, Inc., New York, 1961, pp 81-96; and Hance et al., Weed Control Handbook, 8th Ed., Blackwell Scientific Publications, Oxford, 1989, each of which is incorporated herein by reference in their entirety.
The methods of the invention further allow for the development of herbicide combinations to be used with the DP-305423-1 soybean plants. In such methods, the environmental conditions in an area of cultivation are evaluated. Environmental conditions that can be evaluated include, but are not limited to, ground and surface water pollution concerns, intended use of the crop, crop tolerance, soil residuals, weeds present in area of cultivation, soil texture, pH of soil, amount of organic matter in soil, application equipment, and tillage practices. Upon the evaluation of the environmental conditions, an effective amount of a combination of herbicides can be applied to the crop, crop part, seed of the crop or area of cultivation.
In some embodiments, the herbicide applied to the DP-305423-1 soybean plants of the invention serves to prevent the initiation of growth of susceptible weeds and/or serve to cause damage to weeds that are growing in the area of interest. In some embodiments, the herbicide or herbicide mixture exert these effects on weeds affecting crops that are subsequently planted in the area of interest (i.e., field or area of cultivation). In the methods of the invention, the application of the herbicide combination need not occur at the same time. So long as the field in which the crop is planted contains detectable amounts of the first herbicide and the second herbicide is applied at some time during the period in which the crop is in the area of cultivation, the crop is considered to have been treated with a mixture of herbicides according to the invention. Thus, methods of the invention encompass applications of herbicide which are “preemergent,” “postemergent,” “preplant incorporation” and/or which involve seed treatment prior to planting.
In one embodiment, methods are provided for coating seeds. The methods comprise coating a seed with an effective amount of a herbicide or a combination of herbicides (as disclosed elsewhere herein). The seeds can then be planted in an area of cultivation. Further provided are seeds having a coating comprising an effective amount of a herbicide or a combination of herbicides (as disclosed elsewhere herein).
“Preemergent” refers to a herbicide which is applied to an area of interest (e.g., a field or area of cultivation) before a plant emerges visibly from the soil. “Postemergent” refers to a herbicide which is applied to an area after a plant emerges visibly from the soil. In some instances, the terms “preemergent” and “postemergent” are used with reference to a weed in an area of interest, and in some instances these terms are used with reference to a crop plant in an area of interest. When used with reference to a weed, these terms may apply to only a particular type of weed or species of weed that is present or believed to be present in the area of interest. While any herbicide may be applied in a preemergent and/or postemergent treatment, some herbicides are known to be more effective in controlling a weed or weeds when applied either preemergence or postemergence. For example, rimsulfuron has both preemergence and postemergence activity, while other herbicides have predominately preemergence (metolachlor) or postemergence (glyphosate) activity. These properties of particular herbicides are known in the art and are readily determined by one of skill in the art. Further, one of skill in the art would readily be able to select appropriate herbicides and application times for use with the transgenic plants of the invention and/or on areas in which transgenic plants of the invention are to be planted. “Preplant incorporation” involves the incorporation of compounds into the soil prior to planting.
The time at which a herbicide is applied to an area of interest (and any plants therein) may be important in optimizing weed control. The time at which a herbicide is applied may be determined with reference to the size of plants and/or the stage of growth and/or development of plants in the area of interest, e.g., crop plants or weeds growing in the area. The stages of growth and/or development of plants are known in the art. For example, soybean plants normally progress through vegetative growth stages known as VE (emergence), VC (cotyledon), V1 (unifoliate), and V2 to VN. Soybeans then switch to the reproductive growth phase in response to photoperiod cues; reproductive stages include R1 (beginning bloom), R2 (full bloom), R3 (beginning pod), R4 (full pod), R5 (beginning seed), R6 (full seed), R7 (beginning maturity), and R8 (full maturity). Thus, for example, the time at which a herbicide or other chemical is applied to an area of interest in which plants are growing may be the time at which some or all of the plants in a particular area have reached at least a particular size and/or stage of growth and/or development, or the time at which some or all of the plants in a particular area have not yet reached a particular size and/or stage of growth and/or development.
The term “safener” refers to a substance that when added to a herbicide formulation eliminates or reduces the phytotoxic effects of the herbicide to certain crops. One of ordinary skill in the art would appreciate that the choice of safener depends, in part, on the crop plant of interest and the particular herbicide or combination of herbicides included in the synergistic herbicide composition. Exemplary safeners suitable for use with the presently disclosed herbicide compositions include, but are not limited to, those disclosed in U.S. Pat. Nos. 4,808,208; 5,502,025; 6,124,240 and U.S. Patent Application Publication Nos. 2006/0148647; 2006/0030485; 2005/0233904; 2005/0049145; 2004/0224849; 2004/0224848; 2004/0224844; 2004/0157737; 2004/0018940; 2003/0171220; 2003/0130120; 2003/0078167, the disclosures of which are incorporated herein by reference in their entirety. The methods of the invention can involve the use of herbicides in combination with herbicide safeners such as benoxacor, BCS (1-bromo-4-[(chloromethyl) sulfonyl]benzene), cloquintocet-mexyl, cyometrinil, dichlorm id, 2-(dichloromethyl)-2-methyl-1,3-dioxolane (MG 191), fenchlorazole-ethyl, fenclorim, flurazole, fluxofenim, furilazole, isoxadifen-ethyl, mefenpyr-diethyl, methoxyphenone ((4-methoxy-3-methylphenyl)(3-methylphenyl)-methanone), naphthalic anhydride (1,8-naphthalic anhydride) and oxabetrinil to increase crop safety. Antidotally effective amounts of the herbicide safeners can be applied at the same time as the compounds of this invention, or applied as seed treatments.
Seed treatment is particularly useful for selective weed control, because it physically restricts antidoting to the crop plants. Therefore a particularly useful embodiment of the present invention is a method for selectively controlling the growth of weeds in a field comprising treating the seed from which the crop is grown with an antidotally effective amount of safener and treating the field with an effective amount of herbicide to control weeds. Antidotally effective amounts of safeners can be easily determined by one skilled in the art through simple experimentation. An antidotally effective amount of a safener is present where a desired plant is treated with the safener so that the effect of a herbicide on the plant is decreased in comparison to the effect of the herbicide on a plant that was not treated with the safener; generally, an antidotally effective amount of safener prevents damage or severe damage to the plant treated with the safener. One of skill in the art is capable of determining whether the use of a safener is appropriate and determining the dose at which a safener should be administered to a crop.
In specific embodiments, the combination of safening herbicides comprises a first ALS inhibitor and a second ALS inhibitor.
Such mixtures provide increased crop tolerance (i.e., a decrease in herbicidal injury). This method allows for increased application rates of the chemistries post or pre-treatment. Such methods find use for increased control of unwanted or undesired vegetation. In still other embodiments, a safening affect is achieved when the DP-305423-1 soybean crops, crop part, crop seed, weed, or area of cultivation is treated with at least one herbicide from the sulfonylurea family of chemistry in combination with at least one herbicide from the imidazolinone family. This method provides increased crop tolerance (i.e., a decrease in herbicidal injury). In specific embodiments, the sulfonylurea comprises rimsulfuron and the imidazolinone comprises imazethapyr.
As used herein, an “adjuvant” is any material added to a spray solution or formulation to modify the action of an agricultural chemical or the physical properties of the spray solution. See, for example, Green and Foy (2003) “Adjuvants: Tools for Enhancing Herbicide Performance,” in Weed Biology and Management, ed. Inderjit (Kluwer Academic Publishers, The Netherlands). Adjuvants can be categorized or subclassified as activators, acidifiers, buffers, additives, adherents, antiflocculants, antifoamers, defoamers, antifreezes, attractants, basic blends, chelating agents, cleaners, colorants or dyes, compatibility agents, cosolvents, couplers, crop oil concentrates, deposition agents, detergents, dispersants, drift control agents, emulsifiers, evaporation reducers, extenders, fertilizers, foam markers, formulants, inerts, humectants, methylated seed oils, high load COCs, polymers, modified vegetable oils, penetrators, repellants, petroleum oil concentrates, preservatives, rainfast agents, retention aids, solubilizers, surfactants, spreaders, stickers, spreader stickers, synergists, thickeners, translocation aids, uv protectants, vegetable oils, water conditioners, and wetting agents.
In addition, methods of the invention can comprise the use of a herbicide or a mixture of herbicides, as well as, one or more other insecticides, fungicides, nematocides, bactericides, acaricides, growth regulators, chemosterilants, semiochemicals, repellents, attractants, pheromones, feeding stimulants or other biologically active compounds or entomopathogenic bacteria, virus, or fungi to form a multi-component mixture giving an even broader spectrum of agricultural protection. Examples of such agricultural protectants which can be used in methods of the invention include: insecticides such as abamectin, acephate, acetamiprid, am idoflumet (S-1955), avermectin, azadirachtin, azinphos-methyl, bifenthrin, bifenazate, buprofezin, carbofuran, cartap, chlorfenapyr, chlorfluazuron, chlorpyrifos, chlorpyrifos-methyl, chromafenozide, clothianidin, cyflumetofen, cyfluthrin, beta-cyfluthrin, cyhalothrin, lambda-cyhalothrin, cypermethrin, cyromazine, deltamethrin, diafenthiuron, diazinon, dieldrin, diflubenzuron, dimefluthrin, dimethoate, dinotefuran, diofenolan, emamectin, endosulfan, esfenvalerate, ethiprole, fenothiocarb, fenoxycarb, fenpropathrin, fenvalerate, fipronil, flonicam id, flubendiamide, flucythrinate, tau-fluvalinate, flufenerim (UR-50701), flufenoxuron, fonophos, halofenozide, hexaflumuron, hydramethylnon, imidacloprid, indoxacarb, isofenphos, lufenuron, malathion, metaflumizone, metaldehyde, methamidophos, methidathion, methomyl, methoprene, methoxychlor, metofluthrin, monocrotophos, methoxyfenozide, nitenpyram, nithiazine, novaluron, noviflumuron (XDE-007), oxamyl, parathion, parathion-methyl, permethrin, phorate, phosalone, phosmet, phosphamidon, pirimicarb, profenofos, profluthrin, pymetrozine, pyrafluprole, pyrethrin, pyridalyl, pyriprole, pyriproxyfen, rotenone, ryanodine, spinosad, spirodiclofen, spiromesifen (BSN 2060), spirotetramat, sulprofos, tebufenozide, teflubenzuron, tefluthrin, terbufos, tetrachlorvinphos, thiacloprid, thiamethoxam, thiodicarb, thiosultap-sodium, tralomethrin, triazamate, trichlorfon and triflumuron; fungicides such as acibenzolar, aldimorph, amisulbrom, azaconazole, azoxystrobin, benalaxyl, benomyl, benthiavalicarb, benthiavalicarb-isopropyl, binomial, biphenyl, bitertanol, blasticidin-S, Bordeaux mixture (Tribasic copper sulfate), boscalid/nicobifen, bromuconazole, bupirimate, buthiobate, carboxin, carpropamid, captafol, captan, carbendazim, chloroneb, chlorothalonil, chlozolinate, clotrimazole, copper oxychloride, copper salts such as copper sulfate and copper hydroxide, cyazofamid, cyflunamid, cymoxanil, cyproconazole, cyprodinil, dichlofluanid, diclocymet, diclomezine, dicloran, diethofencarb, difenoconazole, dimethomorph, dimoxystrobin, diniconazole, diniconazole-M, dinocap, discostrobin, dithianon, dodemorph, dodine, econazole, etaconazole, edifenphos, epoxiconazole, ethaboxam, ethirimol, ethridiazole, famoxadone, fenamidone, fenarimol, fenbuconazole, fencaram id, fenfuram, fenhexamide, fenoxanil, fenpiclonil, fenpropidin, fenpropimorph, fentin acetate, fentin hydroxide, ferbam, ferfurazoate, ferimzone, fluazinam, fludioxonil, flumetover, fluopicolide, fluoxastrobin, fluquinconazole, fluquinconazole, flusilazole, flusulfamide, flutolanil, flutriafol, folpet, fosetyl-aluminum, fuberidazole, furalaxyl, furametapyr, hexaconazole, hymexazole, guazatine, imazalil, imibenconazole, iminoctadine, iodicarb, ipconazole, iprobenfos, iprodione, iprovalicarb, isoconazole, isoprothiolane, kasugamycin, kresoxim-methyl, mancozeb, mandipropam id, maneb, mapanipyrin, mefenoxam, mepronil, metalaxyl, metconazole, methasulfocarb, metiram, metominostrobin/fenominostrobin, mepanipyrim, metrafenone, miconazole, myclobutanil, neo-asozin (ferric methanearsonate), nuarimol, octhilinone, ofurace, orysastrobin, oxadixyl, oxolinic acid, oxpoconazole, oxycarboxin, paclobutrazol, penconazole, pencycuron, penthiopyrad, perfurazoate, phosphonic acid, phthalide, picobenzam id, picoxystrobin, polyoxin, probenazole, prochloraz, procymidone, propamocarb, propamocarb-hydrochloride, propiconazole, propineb, proquinazid, prothioconazole, pyraclostrobin, pryazophos, pyrifenox, pyrimethanil, pyrifenox, pyrolnitrine, pyroquilon, quinconazole, quinoxyfen, quintozene, silthiofam, simeconazole, spiroxamine, streptomycin, sulfur, tebuconazole, techrazene, tecloftalam, tecnazene, tetraconazole, thiabendazole, thifluzamide, thiophanate, thiophanate-methyl, thiram, tiadinil, tolclofos-methyl, tolyfluanid, triadimefon, triadimenol, triarimol, triazoxide, tridemorph, trimoprhamide tricyclazole, trifloxystrobin, triforine, triticonazole, uniconazole, validamycin, vinclozolin, zineb, ziram, and zoxamide; nematocides such as aldicarb, oxamyl and fenamiphos; bactericides such as streptomycin; acaricides such as amitraz, chinomethionat, chlorobenzilate, cyhexatin, dicofol, dienochlor, etoxazole, fenazaquin, fenbutatin oxide, fenpropathrin, fenpyroximate, hexythiazox, propargite, pyridaben and tebufenpyrad; and biological agents including entomopathogenic bacteria, such as Bacillus thuringiensis subsp. Aizawai, Bacillus thuringiensis subsp. Kurstaki, and the encapsulated delta-endotoxins of Bacillus thuringiensis (e.g., Cellcap, MPV, MPVII); entomopathogenic fungi, such as green muscardine fungus; and entomopathogenic virus including baculovirus, nucleopolyhedro virus (NPV) such as HzNPV, AfNPV; and granulosis virus (GV) such as CpGV. The weight ratios of these various mixing partners to other compositions (e.g., herbicides) used in the methods of the invention typically are between 100:1 and 1:100, or between 30:1 and 1:30, between 10:1 and 1:10, or between 4:1 and 1:4.
The present invention also pertains to a composition comprising a biologically effective amount of a herbicide of interest or a mixture of herbicides, and an effective amount of at least one additional biologically active compound or agent and can further comprise at least one of a surfactant, a solid diluent or a liquid diluent. Examples of such biologically active compounds or agents are: insecticides such as abamectin, acephate, acetamiprid, amidoflumet (S-1955), avermectin, azadirachtin, azinphos-methyl, bifenthrin, binfenazate, buprofezin, carbofuran, chlorfenapyr, chlorfluazuron, chlorpyrifos, chlorpyrifos-methyl, chromafenozide, clothianidin, cyfluthrin, beta-cyfluthrin, cyhalothrin, lambda-cyhalothrin, cypermethrin, cyromazine, deltamethrin, diafenthiuron, diazinon, diflubenzuron, dimethoate, diofenolan, emamectin, endosulfan, esfenvalerate, ethiprole, fenothicarb, fenoxycarb, fenpropathrin, fenvalerate, fipronil, flonicam id, flucythrinate, tau-fluvalinate, flufenerim (UR-50701), flufenoxuron, fonophos, halofenozide, hexaflumuron, imidacloprid, indoxacarb, isofenphos, lufenuron, malathion, metaldehyde, methamidophos, methidathion, methomyl, methoprene, methoxychlor, monocrotophos, methoxyfenozide, nithiazin, novaluron, noviflumuron (XDE-007), oxamyl, parathion, parathion-methyl, permethrin, phorate, phosalone, phosmet, phosphamidon, pirimicarb, profenofos, pymetrozine, pyridalyl, pyriproxyfen, rotenone, spinosad, spiromesifin (BSN 2060), sulprofos, tebufenozide, teflubenzuron, tefluthrin, terbufos, tetrachlorvinphos, thiacloprid, thiamethoxam, thiodicarb, thiosultap-sodium, tralomethrin, trichlorfon and triflumuron; fungicides such as acibenzolar, azoxystrobin, benomyl, blasticidin-S, Bordeaux mixture (tribasic copper sulfate), bromuconazole, carpropamid, captafol, captan, carbendazim, chloroneb, chlorothalonil, copper oxychloride, copper salts, cyflufenam id, cymoxanil, cyproconazole, cyprodinil, (S)-3,5-dichloro-N-(3-chloro-1-ethyl-1-methyl-2-oxopropyl)-4-methylbenzamide (RH 7281), diclocymet (S-2900), diclomezine, dicloran, difenoconazole, (S)-3,5-dihydro-5-methyl-2-(methylthio)-5-phenyl-3-(phenyl-amino)-4H-im idazol-4-one (RP 407213), dimethomorph, dimoxystrobin, diniconazole, diniconazole-M, dodine, edifenphos, epoxiconazole, famoxadone, fenamidone, fenarimol, fenbuconazole, fencaramid (SZX0722), fenpiclonil, fenpropidin, fenpropimorph, fentin acetate, fentin hydroxide, fluazinam, fludioxonil, flumetover (RPA 403397), flumorf/flumorlin (SYP-L190), fluoxastrobin (HEC 5725), fluquinconazole, flusilazole, flutolanil, flutriafol, folpet, fosetyl-aluminum, furalaxyl, furametapyr (S-82658), hexaconazole, ipconazole, iprobenfos, iprodione, isoprothiolane, kasugamycin, kresoxim-methyl, mancozeb, maneb, mefenoxam, mepronil, metalaxyl, metconazole, metomino-strobin/fenominostrobin (SSF-126), metrafenone (AC375839), myclobutanil, neo-asozin (ferric methane-arsonate), nicobifen (BAS 510), orysastrobin, oxadixyl, penconazole, pencycuron, probenazole, prochloraz, propamocarb, propiconazole, proquinazid (DPX-KQ926), prothioconazole (JAU 6476), pyrifenox, pyraclostrobin, pyrimethanil, pyroquilon, quinoxyfen, spiroxamine, sulfur, tebuconazole, tetraconazole, thiabendazole, thifluzamide, thiophanate-methyl, thiram, tiadinil, triadimefon, triadimenol, tricyclazole, trifloxystrobin, triticonazole, validamycin and vinclozolin; nematocides such as aldicarb, oxamyl and fenamiphos; bactericides such as streptomycin; acaricides such as amitraz, chinomethionat, chlorobenzilate, cyhexatin, dicofol, dienochlor, etoxazole, fenazaquin, fenbutatin oxide, fenpropathrin, fenpyroximate, hexythiazox, propargite, pyridaben and tebufenpyrad; and biological agents including entomopathogenic bacteria, such as Bacillus thuringiensis subsp. Aizawai, Bacillus thuringiensis subsp. Kurstaki, and the encapsulated delta-endotoxins of Bacillus thuringiensis (e.g., Cellcap, MPV, MPVII); entomopathogenic fungi, such as green muscardine fungus; and entomopathogenic virus including baculovirus, nucleopolyhedro virus (NPV) such as HzNPV, AfNPV; and granulosis virus (GV) such as CpGV. Methods of the invention may also comprise the use of plants genetically transformed to express proteins toxic to invertebrate pests (such as Bacillus thuringiensis delta-endotoxins). In such embodiments, the effect of exogenously applied invertebrate pest control compounds may be synergistic with the expressed toxin proteins.
General references for these agricultural protectants include The Pesticide Manual, 13th Edition, C. D. S. Tomlin, Ed., British Crop Protection Council, Farnham, Surrey, U.K., 2003 and The BioPesticide Manual, 2nd Edition, L. G. Copping, Ed., British Crop Protection Council, Farnham, Surrey, U.K., 2001.
In certain instances, combinations with other invertebrate pest control compounds or agents having a similar spectrum of control but a different mode of action will be particularly advantageous for resistance management. Thus, compositions of the present invention can further comprise a biologically effective amount of at least one additional invertebrate pest control compound or agent having a similar spectrum of control but a different mode of action. Contacting a plant genetically modified to express a plant protection compound (e.g., protein) or the locus of the plant with a biologically effective amount of a compound of this invention can also provide a broader spectrum of plant protection and be advantageous for resistance management.
Thus, methods of the invention employ a herbicide or herbicide combination and may further comprise the use of insecticides and/or fungicides, and/or other agricultural chemicals such as fertilizers. The use of such combined treatments of the invention can broaden the spectrum of activity against additional weed species and suppress the proliferation of any resistant biotypes.
Methods of the invention can further comprise the use of plant growth regulators such as aviglycine, N-(phenylmethyl)-1H-purin-6-amine, ethephon, epocholeone, gibberellic acid, gibberellin A4 and A7, harpin protein, mepiquat chloride, prohexadione calcium, prohydrojasmon, sodium nitrophenolate and trinexapac-methyl, and plant growth modifying organisms such as Bacillus cereus strain BP01.
Embodiments of the present invention are further defined in the following Examples. It should be understood that these Examples are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the embodiments of the invention to adapt it to various usages and conditions. Thus, various modifications of the embodiments of the invention, in addition to those shown and described herein, will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims.
EXAMPLE 1 Genetic Material Used to Produce the DP-305423-1 EventSoybean (Glycine max) event DP-305423-1 was produced by particle co-bombardment with fragments PHP19340A (
The PHP19340A fragment contains a cassette with a 597 bp fragment of the soybean microsomal omega-6 desaturase gene 1 (gm-fad2-1) (Heppard et al., 1996). The presence of the gm-fad2-1 fragment in the expression cassette acts to suppress expression of the endogenous omega-6 desaturases, resulting in an increased level of oleic acid and decreased levels of palmitic, linoleic, and linolenic acid levels. Upstream of the gm-fad2-1 fragment is the promoter region from the Kunitz trypsin inhibitor gene 3 (KTi3) (Jofuku and Goldberg, 1989; Jofuku et al., 1989) regulating expression of the transcript. The KTi3 promoter is highly active in soy embryos and 1000-fold less active in leaf tissue (Jofuku and Goldberg, 1989). The 3′ untranslated region of the KTi3 gene (KTi3 terminator) (Jofuku and Goldberg, 1989) terminates expression from this cassette.
The PHP17752A fragment contains a cassette with a modified version of the soybean acetolactate synthase gene (gm-hra) encoding the GM-HRA protein with two amino acid residues modified from the endogenous enzyme and five additional amino acids at the N-terminal region of the protein derived from the translation of the soybean acetolactate synthase gene 5′ untranslated region (Falco and Li, 2003). The gm-hra gene encodes a form of acetolactate synthase, which is tolerant to the sulfonylurea class of herbicides. The GM-HRA protein is comprised of 656 amino acids and has a molecular weight of approximately 71 kDa.
The expression of the gm-hra gene is controlled by the 5′ promoter region of the S-adenosyl-L-methionine synthetase (SAMS) gene from soybean (Falco and Li, 2003). This 5′ region consists of a constitutive promoter and an intron that interrupts the SAMS 5′ untranslated region (Falco and Li, 2003). The terminator for the gm-hra gene is the endogenous soybean acetolactate synthase terminator (gm-als terminator) (Falco and Li, 2003).
Dunn, J. J. and Studier, F. W. 1983. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol 166(4): 477-535.
Falco, C. S. and Li, Z. 2003. S-adenosyl-L-methionine Synthetase Promoter and Its Use in Expression of Transgenic Genes in Plants. US Patent Application: 2003/0226166.
Gritz, L. and Davies, J. 1983. Plasmid-encoded hygromycin B resistance: the sequence of hygromycin B phosphotransferase gene and its expression in E. coli and Saccharomyces cerevisiae. Gene 25: 179-188.
Heppard, E. P., Kinney, A. J., Stecca, K. L., and Miao, G.-H. 1996. Developmental and Growth Temperature Regulation of Two Different Microsomal omega-6 Desaturase Genes in Soybeans. Plant Physiol. 110: 311-319.
Jofuku, K. D. and Goldberg, R. B. 1989. Kunitz Trypsin Inhibitor Genes Are Differentially Expressed during the Soybean Life Cycle and in Transformed Tobacco Plants. Plant Cell 1: 1079-1093.
Jofuku, K. D. and Schipper, R. D. and Goldberg, R. B. 1989. A Frameshift Mutation Prevents Kunitz Trypsin Inhibitor mRNA Accumulation in Soybean Embryos. Plant Cell 1: 427-435.
Tomizawa, J-I., Ohmori, H., and Bird, R. E. 1977. Origin of replication of colicin E1 plasmid DNA. Proc. Natl. Acad. Sci. 74 (5): 1865-1869.
EXAMPLE 2 Method of Transformation and Selection for the Soybean Event DP-305423-1For transformation of soybean tissue, a linear portion of DNA, containing the gm-fad2-1 gene sequence and the regulatory components necessary for expression, was excised from the plasmid PHP19340 through the use of the restriction enzyme Asc I and purified using agarose gel electrophoresis. A linear portion of DNA, containing the gm-hra gene sequences and the regulatory components necessary for expression, was excised from the plasmid PHP17752 through the use of the restriction enzyme Asc I and purified using agarose gel electrophoresis. The linear portion of DNA containing the gm-fad2-1 gene is designated insert PHP19340A and is 2924 bp in size. The linear portion of DNA containing the gm-hra gene is designated insert PHP17752A and is 4511 bp in size. The only DNA introduced into transformation event DP-305423-1 was the DNA of the inserts described above.
The transgenic plants from event DP-305423-1 were obtained by microprojectile bombardment using the Biolistics™ PDS-1000He particle gun manufactured by Bio-Rad, essentially as described by Klein et al. (“High velocity microprojectiles for delivering nucleic acids into living cells”, Nature 327:70-73 (1987)). The targets for transformation were clumps of secondary somatic embryos derived from explants from small, immature soybean seeds. The secondary somatic embryos were excised from immature explants after several weeks on a soybean culture initiation medium. The embryogenic clumps which were excised from the explants were transferred to a liquid soybean culture maintenance medium, and subcultured at regular intervals until prepared for bombardment.
Soybean somatic embryogenic cultures are used in transformation experiments from 2-4 months after initiation. On the day of transformation, microscopic gold particles were coated with a mixture of the DNA of the two purified fragments, PHP19340A and PHP17752A, and accelerated into the embryogenic soybean cultures, after which the insert DNAs were incorporated into some of the cells' chromosomes. Only PHP19340A and PHP17752A were used and no additional DNA (e.g., carrier DNA) was incorporated into the transformation process. After bombardment, the bombarded soybean tissue was transferred to flasks of fresh liquid culture maintenance medium for recovery. After a few days, the liquid culture medium in each flask of bombarded embryogenic soybean culture was changed to culture maintenance medium supplemented with chlorsulfuron as the selection agent. Individual flasks of tissue in liquid selective medium were kept physically separate during culture, and the majority of the somatic embryogenic clumps within each flask died in the liquid selective medium.
After several weeks in the culture maintenance medium supplemented with chlorsulfuron, small islands of healthy, chlorsulfuron-resistant green tissue became visible growing out of pieces of dying somatic embryogenic tissue. The resistant embryogenic clumps were excised from their associated pieces of dying or dead tissue, and were assigned unique identification codes representing putative transformation events. The individual putative events received regular changes to fresh liquid selection medium until the start of the regeneration process. Embryogenic tissue samples were taken for molecular analysis to confirm the presence of the gm-fad2-1 and gm-hra transgenes by Southern analysis. Plants were regenerated from tissue derived from each unique event and transferred to the greenhouse for seed production.
EXAMPLE 3 Southern Analysis of Plants Containing the DP-305423-1 EventMaterials and Methods: Genomic DNA was extracted from frozen soybean leaf tissue of individual plants of the T4 and T5 generations of DP-305423-1 and of control (variety: Jack) using a standard Urea Extraction Buffer method. Genomic DNA was quantified on a spectrofluorometer using Pico Green® reagent (Molecular Probes, Invitrogen). Approximately 4μg of DNA per sample was digested with Hind III or Nco I. For positive control samples, approximately 3 pg (2 genome copy equivalents) of plasmid PHP19340 or PHP17752 was added to control soybean genomic DNA prior to digestion. Negative control samples consisted of unmodified soybean genomic DNA (variety: Jack). DNA fragments were separated by size using agarose gel electrophoresis.
Following agarose gel electrophoresis, the separated DNA fragments were depurinated, denatured, neutralized in situ, and transferred to a nylon membrane in 20× SSC buffer using the method as described for TURBOBLOTTER™ Rapid Downward Transfer System (Schleicher & Schuell). Following transfer to the membrane, the DNA was bound to the membrane by UV crosslinking.
DNA probes for gm-fad2-1 and gm-hra were labeled with digoxigenin (DIG) by PCR using the PCR DIG Probe Synthesis Kit (Roche).
Labeled probes were hybridized to the target DNA on the nylon membranes for detection of the specific fragments using DIG Easy Hyb solution (Roche) essentially as described by manufacturer. Post-hybridization washes were carried out at high stringency. DIG-labeled probes hybridized to the bound fragments were detected using the CDP-Star Chemiluminescent Nucleic Acid Detection System (Roche). Blots were exposed to X-ray film at room temperature for one or more time points to detect hybridizing fragments.
Summary of Southern Analysis of DP-305423-1: Schematic maps of plasmids PHP19340 (SEQ ID NO:3) and PHP17752 (SEQ ID NO:4) used as positive controls on these blots are presented in
Genomic DNA isolated from soybean leaf tissue of individual plants of DP-305423-1 (T5 and T4 generation) and of unmodified control (Jack) was digested with Hind III and probed with the gm-fad2-1 gene probe (
Genomic DNA isolated from soybean leaf tissue of individual plants of DP-305423-1 (T5 and T4 generation) and of unmodified control (Jack) was digested with Nco I and probed with the gm-fad2-1 gene probe (
Genomic DNA isolated from soybean leaf tissue of individual plants of DP-305423-1 (T5 and T4 generation) and of unmodified control (Jack) was digested with Hind III and probed with the gm-hra gene probe (
Genomic DNA isolated from soybean leaf tissue of individual plants of DP-305423-1 (T5 and T4 generation) and of unmodified control (Jack) was digested with Nco I and probed with the gm-hra gene probe. Approximately 2 pg of genomic DNA was digested and loaded per lane. The gene copy number controls included plasmid PHP19340 and PHP17752 at the indicated approximate gene copy number and 2 μg of unmodified control DNA. Sizes of the DIG VII molecular weight markers are indicated adjacent to the blot image in kilobase pairs (kb). A description of each lane is presented in Table 10.
Tables 11 and 12 summarize the results from the Southern blot analyses presented in
Hind III digestions were conducted on the genomic DNA samples to evaluate internal fragments and integrity of both PHP19340A (
The gm-fad2-1 and gm-hra probes used for Southern analysis were highly homologous to sequences in the endogenous soybean genome and thus additional hybridizing fragments were expected. These hybridizing bands were determined by their presence in the negative control samples and are indicated in Tables 11 and 12 by an asterisk (*).
To verify the integrity of the 3′ region of the PHP19340A insertion, the gm-fad2-1 was hybridized to the Hind III blot. A single internal fragment of 1687 bp would be expected based on the presence of Hind III sites in PHP19340A (Table 11,
To determine the number of copies of the gm-fad2-1 element in DP-305423-1, the gm-fad2-1 probe was hybridized to the Nco I blot. A border fragment of greater than 2300 bp would be expected for each copy gm-fad2-1 (Table 11,
Hybridization of the gm-hra probe to the Hind III blot would verify the integrity of the inserted PHP17752A fragment as two internal bands of 1529 bp and 2418 bp would be expected based on the position of Hind III sites on the fragment (Table 12,
Hybridization of the gm-hra probe to the Nco I blot would verify the number of copies of the element in DP-305423-1. Two border fragments, one greater than 1500 bp and a second greater than 3000 bp, would be expected for each copy of the element based on the position of the Nco I restriction enzyme site within the gm-hra gene in PHP17752A (Table 12,
In summary, these restriction enzyme and probe combinations showed consistent hybridization patterns throughout all individuals analyzed and across the T4 and T5 generations of DP-305423-1. Based on the analyses reported here, there appear to be approximately six copies of the partial or complete gm-fad2-1 element and a single copy of the gm-hra gene in the genome of DP-305423-1. Intact and partial copies of PHP19340A and a single intact copy of PHP17752A are likely to have inserted into the genome of DP-305423-1.
EXAMPLE 4 Confirmation of High Oleic Acid Phenotype by Gas Chromatography (CG) and Southern Blot AnalysisPrior to planting, remove small seed chips (˜2 mg) from the seed cotyledons using a razor blade. Prepare fatty acid methyl esters (FAMES) from single, matured, soybean seed chips by transesterification using trimethylsulfonium hydroxide (TMSH) (Butte, 1983). Place seed chips in a 1.5 mL glass gas chromatography vial containing 50 μL of TMSH and 0.5 mL of heptane and incubate for 10 minutes at room temperature while shaking. Transfer vials to the vial racks on the Gas Chromatograph. Separate and quantify fatty acid methyl esters (3 μL injected from heptane layer) using a Hewlett-Packard 6890-2 Gas Chromatograph fitted with an Omegawax 320 fused silica capillary column (Supelco Inc., Bellfonte, PA) and a Flame Ionization Detector (FID). The oven temperature is programmed to hold at 220° C. for 5 min, increase to 240° C. at 20° C./min and hold for an additional minute. A Whatman hydrogen generator supplies carrier gas and supplies hydrogen for the FID. Retention times are compared to those for methyl esters of commercially available standards (Nu-Chek Prep, Inc., Elysian, Minn.).
Oil profiles for all seeds are reviewed for elevated oleic acid (18:1) levels as confirmation of the phenotype. The oleic acid level as measured by GC is expected to be >70% for DP-305423-1 soybean seeds, and <30% for the control seeds.
Plants are examined by Southern blot analysis to confirm the presence of the introduced gm-fad2-1 gene fragment and gm-hra gene in DP-305423-1 soybean plants, their absence in control soybean plants, and these data are correlated with the oleic acid results.
EXAMPLE 5 Characterization of Insert and Flanking Border Sequence of Soybean Event DP-305423-1The insert and flanking border regions of DP-305423-1 genomic DNA were isolated by PCR amplification and by cosmid cloning. PCR fragments were either sequenced directly or cloned into plamid vectors prior to sequencing. Cosmid DNAs were isolated and sequenced.
Partial and intact copies of PHP19340A and a single copy of PHP17752A were found to be present on four contigs of genomic DNA from the DP-305423-1 event. These four contigs were designated Contig-1 (
Genomic DNA Cloning and Primer Design:
Total genomic DNA from DP-305423-1 soybean was partially digested with restriction enzymes HindIII and MboI, and cloned into cosmid vectors to construct HindIII and MboI cosmid libraries. The cosmid libraries were screened using a KTi3 promoter fragment as probe. Total three unique clones (51-21, 51-9, and H3IIBB19) were identified from Hindil library, and two (mbo30 and mbo22) from MboI library. These five clones were analyzed by full-insert sequencing (FIS), a transposon-based sub-cloning method to facilitate bi-directional sequencing of a cloned insert from the site of the transposition event (MJ Research TGS system; Happa et al., 1999). Sequence analysis showed that 51-21 and mbo30 were overlap clones containing the identical insertion from Contig-1, 51-9 and mbo22 were overlap clones containing the identical insertion from Contig-2, and H3IIBB19 contained unique Contig-3. Primers were designed based on the sequences from the cosmid clones. Genomic PCR was performed to verify the insertions and flanking border regions in DP-305423-1 soybean.
Contig-1—Insert and Flanking Genomic Border Regions:
Primers were designed based on the sequence information obtained from the cosmid clones 51-21 and mbo30 containing sequence of Contig-1. PCR products were amplified from genomic DNA of DP-305423-1 soybean using primer pairs A (06-O-1571/06-O-1572, 7103 bp of 5′ insert/genomic border junction), B (06-O-1351/06-O-1367, 731 bp of 5′ insert/border junction), C (06-O-1357/06-O-1368, 3226 bp of insert), D (06-O-1357/06-O-1369, 2737 bp of insert), E (06-O-1356/06-O-1371, 1800 bp of insert), F (06-O-1360/06-O-1423, 1321 bp of insert), G (06-O-1363/06-O-06-O-1369, 1830 bp of insert), H (06-O-1421/06-O-06-O-1367, 2410 b p of insert), and I (06-O-1577/06-O-1578, 2991 bp of 3′ insert/genomic border junction) (Table 13), and cloned. PCR products B, C, D, E, F, G, and H were directly sequenced to verify the insertion, and A and I were analyzed by FIS to verify 5′ and 3′ insert/genomic junctions and their flanking border regions. No PCR products were amplified when the control genomic DNA was used as a template.
For Contig-1, 22452 bp of DP-305423-1 genomic sequence was confirmed (nucleotides 11652-34103 of SEQ ID NO:5), comprising 7000 bp of the 5′ flanking border sequence, 2524 bp of the 3′ flanking genomic border sequence, and 12928 bp of inserted DNA. The insert was found to contain one intact PHP19340A fragment, a single, intact PHP17752A fragment, and three truncated PHP19340A fragments. The first truncated PHP19340A fragment contains a partial KTi3 terminator (180 bp) with 3′ deletion, an intact gm-fad2-1 fragment (597 bp) and an intact KTi3 promoter (2084 bp). The second truncated PHP19340A fragment contains a partial gm-fad2-1 fragment (39 bp) with 3′ deletion and an intact KTi3 promoter (2084 bp). The third truncated PHP19340A fragment contains a partial KTi3 promoter (245 bp) with 5′ deletion and a partial gm-fad2-1 fragment (186 bp) with 3′ deletion.
To demonstrate that the identified 5′ and 3′ flanking border sequences for Contig-1 are of soybean origin, PCR was performed within the 5′ and 3′ flanking border regions (07-O-1889/07-O-1940, 07-O-1892/07-O-1894, respectively) on both DP-305423-1 soybean genomic DNA samples and control samples. The expected PCR products (115 bp for the 5′ flanking genomic region and 278 bp for the 3′ flanking genomic region) were generated from both DP-305423-1 soybean and control samples, indicating that the sequences were of soybean genomic origin and not specific to DP-305423-1 soybean. These PCR products were cloned and sequenced. The sequences from both the DP-305423-1 and control genomic DNA were identical.
Contig-2—Insert and Flanking Genomic Border Regions:
Primers were designed based on the sequence information obtained from the cosmid clones 51-9 and mbo22 for Contig-2. PCR products were amplified from genomic DNA of DP-305423-1 soybean using primer pairs J (06-O-1588/06-O-1585, 7642 bp of 5′ insert/genomic border junction), K (06-O-1586/06-O-1403, 2807 bp of 5′ insert/genomic border junction), and L (06-O-1404/06-O-1592, 2845 bp of 3′ insert/genomic border junction) (Table 13), and cloned. PCR products K and L were directly sequenced to verify the insertion and 3′ insert/genomic border junction and its flanking border region, and J was analyzed by FIS to verify 5′ insert/genomic border junctions and its flanking border region. No PCR products were amplified when the control genomic DNA was used as a template.
For Contig-2, 12667 bp of DP-305423-1 genomic sequence was confirmed (nucleotides 4565-17231 of SEQ ID NO:6), comprising 7599 bp of the 5′ flanking genomic border sequence, 2737 bp of the 3′ flanking genomic border sequence, and 2331 bp of inserted DNA. The insert was found to contain one truncated PHP19340A fragment, with a partial KTi3 promoter (1511 bp), an intact gm-fad2-1 fragment (597 bp), and an intact KTi3 terminator (196 bp).
To demonstrate that the identified 5′ and 3′ flanking border sequences for Contig-2 are of soybean origin, PCR was performed within the 5′ and 3′ flanking genomic regions (primer pairs 07-O-1895/07-O-1898 and 07-O-1905/07-O-1903, respectively) on both DP-305423-1 and control soybean genomic DNA samples. The expected PCR products (278 bp for the 5′ flanking border region and 271 bp for the 3′ flanking border region) were generated from both DP-305423-1 soybean and control samples, indicating that the sequences were of soybean genomic origin and not specific to DP-305423-1 soybean. These PCR products were cloned and sequenced. The sequences from both the DP-305423-1 and control genomic DNA were identical.
Contig-3—Insert and Flanking Genomic Border Regions:
Primers were designed based on the sequence information obtained from the cosmid clone H3IIB19 for Contig-3. PCR products were amplified on genomic DNA from DP-305423-1 using primer pairs M (06-O-1669/06-O-1426, 2804 bp), N (06-O-1355/06-O-1459, 1335 bp), O (06-O-1569/06-O-1551, 1085 bp), and P (05-O-1182/06-O-1672, 2614 bp) (Table 13), and cloned. PCR products M, N, O, and P were directly sequenced to verify the insertion, and the 5′ and 3′ insert/genomic junction and their flanking genomic regions. No PCR products were amplified when the control genomic DNA was used as a template.
For Contig-3, 6789 bp of DP-305423-1 soybean genomic sequence was confirmed (nucleotides 3312-10100 of SEQ ID NO:7), comprising 2439 bp of the 5′ flanking border sequence, 2287 bp of the 3′ flanking border sequence, and 2063 bp of inserted DNA. The insert was found to contain one truncated PHP19340A fragment with only a partial KTi3 promoter (1550 bp), and a 495 bp plasmid backbone fragment. This plasmid backbone fragment was identical to the regions located from 2033 bp to 2527 bp in plasmid PHP19340 and from 1836 bp to 2330 bp in plasmid PHP17752, not including the origin of replication (ori). The ori in plasmids PHP13940 and PHP1772 is located from 1561 to 1930 bp and 1364 to 1733 bp, respectively (Tomizawa et al., 1977).
To demonstrate that the identified 5′ and 3′ flanking border sequences for Contig-3 are of soybean origin, PCR was performed within the 5′ and 3′ flanking border regions (primer pairs 07-O-1881/07-O-1882 and 07-O-1886/07-O-1884, respectively) on both DP-305423-1 soybean genomic DNA samples and control samples. The expected PCR products (262 bp for the 5′ flanking border region and 280 bp for the 3′ flanking border region) were generated from both DP-305423-1 soybean and control samples, indicating that the sequences were of soybean genomic origin and not specific to DP-305423-1 soybean. These PCR products were cloned and sequenced. The sequences from both the DP-305423-1 and control genomic DNA were identical.
Contg-4—Insert and Flanking Genomic Border Regions:
Plasmid libraries and iPCR were used to identify the insert within and the flanking border regions of Contig-4. Total genomic DNA from DP-305423-1 soybean was digested with restriction enzymes SpeI and BcII, and run on agarose gels to separate the DNA fragments based on their molecular weights. The DNA fragments on agarose gels were transferred to nylon membrane, and hybridized with a gm-fad2-1 probe or a KTi3 promoter probe. The 2.8 kb and 5.1 kb bands were hybridized with the gm-fad2-1 probe after SpeI digestion, and 1.5 kb and 3.3 kb bands were hybridized with the KTi3 promoter probe after BO digestion. All of these bands were only present in DP-305423-1 plants, but absent in control plants. These four bands were cloned into plasmid vectors to make plasmid libraries. Positive clones were identified after plasmid library screening with the gm-fad2-1 probe or the KTi3 promoter probe, and were directly sequenced. The sequence for Contig-4 is presented in SEQ ID NO:82.
The 2.8 kb band from SpeI digestion and the 3.3 kb band from BclI digestion were overlapping (referred to as SpeI2.8), containing one truncated PHP19340A fragment with 159 bp deletion at 3′ end of the KTi3 promoter; and the 5.1 band from SpeI digestion and the 1.5 kb band from BclI digestion were overlapping (referred to as SpeI5.1), containing one truncated PHP19340A fragment with 649 bp deletion at 3′ end of the KTi3 promoter. Since there is a SpeI site within the KTi3 terminator, only 148 bp KTi3 terminator sequence was obtained for both SpeI2.8 and SpeI5.1.
Based on the sequence information, primers designed for inverse PCR (iPCR) were used to obtain additional sequence information at the 3′ end of the KTi3 terminator. The iPCR products were either directly sequenced, or cloned and then directly sequenced. Sequence data generated from iPCR products with NdeI digestion showed that SpeI2.8 contained an intact KTi3 terminator and 35 bp KTi3 terminator in the reverse orientation, and SpeI5.1 contained an intact KTi3 terminator and 34 bp KTi3 terminator in the reverse orientation, indicating that the two KTi3 terminators of SpeI2.8 and SpeI5.1 arranged as inverted repeats. Sequence data generated from iPCR products with Pacl digestion confirmed that SpeI2.8 and Spe5.1 are arranged as inverted repeats.
Additional confirmation was done using Southern blot analysis. Total genomic DNA from DP-305423-1 and control soybean plants were digested with BclI, ClaI and XmnI, run on an agarose gel, transferred to nylon membrane, and hybridized with the gm-fad2-1 probe. The predicted size bands were hybridized with the gm-fad2-1 probe: about 3.1 kb band for BclI digestion, about 3.9 kb band for ClaI digestion, and 1.7 kb band for XmnI digestion (
For Contig-4, 10058 bp of DP-305423-1 genomic sequence was identified (SEQ ID NO:82), comprising 2899 bp of the 5′ flanking genomic border sequence, 2149 bp of the 3′ flanking genomic border sequence, and 5010 bp of inserted DNA. The insert was believed to contain two truncated PHP19340A fragments in inverted fashion. The first truncated PHP1930A fragment is located from 2900 to 5163 bp, containing a partial KTi3 promoter (1442 bp) with 5′ deletion, an intact gm-fad2-1 fragment (597 bp) and an intact KTi3 terminator (196 bp). The second truncated PHP1930A fragment is located from 5164 to 7919 bp, containing a partial KTi3 promoter (1934 bp) with 5′ deletion, an intact gm-fad2-1 fragment (597 bp) and an intact KTi3 terminator (196 bp) (
To verify the 5′ and 3′ insert/genomic junctions obtained from plasmid libraries, PCR was performed on genomic DNA of DP-305423-1 soybean plants using primer pair Q (HOS-A/HOS-B) to confirm the 5′ insert/genomic junction, and primer pair R (HOS-C/HOS-D) to confirm the 3′ insert/junction. The expected PCR products were amplified from DP-305423-1 plants (Table 13), and not from control plants; these PCR products were cloned and sequenced. The sequence was confirmed to be the same as the sequence obtained from plasmid clones.
The insert in Contig-1 was found to contain one intact PHP19340A fragment (gm-fad2-1 suppression cassette), a single, intact PHP17752A fragment (gm-hra expression cassette), and three truncated PHP19340A fragments. Southern blot analysis conducted on 100 plants from the F2 generation of DP-305423-1 identified a single plant that appeared to have undergone a recombination event that resulted in the removal of the entire gm-hra cassette along with portions of two of the multiple KTi3 promoter fragments found in the insertion. A large number of plants from segregating generations were analyzed by Polymerase Chain Reaction (PCR) to determine at what frequency this recombination occurs.
Seed was obtained from soybean DP-305423-1 segregating generations BC1F2, BC2F2, and BC3F2. Each generation consisted of DP-305423-1 in either the Elite 1 or Elite 2 background. A total of 1060 seeds were planted (Table 14).
Single leaf punches were collected from plants and genomic DNA was extracted from the punches utilizing a hot sodium hydroxide and tris extraction method (Truett, G. E., Heeger, P., Mynatt, R. L., Truett, A. A., Walker, J. A. and Warman, M. L. (2000) Preparation of PCR-Quality Mouse Genomic DNA with Hot Sodium Hydroxide and Tris (HotSHOT). BioTechniques 29: 52-53.).
Real-time PCR was performed on each DNA sample utilizing an ABI PRISM® 7900HT Sequence Detection System and accompanying SDS software (Applied Biosystems, Inc., Foster City, Calif.). TaqMan® probe and primer sets were designed to detect two insertion target sequences: (1) the 5′ junction region between genomic and insert DNA in Contig-1, which was used as a marker for the gm-fad2-1 suppression cassette (SEQ ID NOs: 26, 27 and 28), and (2) the region in the insert of Contig-1 spanning the SAMS promoter and gm-hra (SEQ ID NOs: 89, 90 and 34). In addition, a TaqMan® probe and primer set for a reference soybean endogenous gene was used to confirm the presence of amplifiable DNA in each reaction. The analysis consisted of quantitative real-time PCR determination of qualitative positive/negative calls. The extracted DNA was assayed using optimized and validated primer and probe concentrations in Extract-N-Amp™ PCR reaction mix containing Rox passive reference dye (Sigma-Aldrich, St. Louis, Mo.). After initial incubations at 50° C. for 2 minutes and then at 95° C. for 3 minutes, 40 cycles were conducted as follows: 95° C. for 15 seconds, 60° C. for 1 minute. Positive or negative determination for each insertion target was based on comparison of the CT (threshold cycle) of the insertion target PCR to that of the endogenous target.
A total of 1009 plants of three different segregating generations (BC1F2, BC2F2 and BC3F2) and two different backgrounds (Elite 1 and Elite 2) were analyzed by qualitative real-time PCR for the Contig-1 5′ junction and the SAMS Promoter::gm-hra targets. Each reaction contained amplifiable DNA based on the endogenous gene control. Of the 1009 plants in the six segregating populations, 745 were positive and 264 were negative for both PCR assays. No plants were identified in which the PCR results were positive for one target and negative for the other. Consequently, in this sample group of 1009 plants, no recombination within the Contig-1 insertion was detected that selectively removed the SAMS Promoter::gm-hra cassette. A summary of the results is given in Table 15.
Levels of 25 fatty acids were measured in DP-305423-1 and control soybean grain. Levels of ten fatty acids were below the lower limit of quantitation (LLOQ) for the assay: caprylic acid (C8:0), capric acid (C10:0), lauric acid (C12:0), myristoleic acid (C14:1), pentadecanoic acid (C15:0), pentadecenoic acid (C15:1), y-linolenic acid (C18:3), eicosatrienoic acid (C20:3), arachidonic acid (C20:4), and erucic acid
(C22:1). Therefore, no statistical analyses were conducted on these fatty acids and data are not shown. Results of the analysis for the 15 remaining fatty acid are presented in Table 16.
The mean values for oleic acid (C18:1) and linoleic acid (C18:2) fell outside the tolerance intervals and/or the combined literature ranges for conventional soybean varieties. As expected, the mean level of the oleic acid in DP-305423-1 soybean was above the upper range of both the statistical tolerance interval for the reference soybean lines and literature range for conventional soybean varieties. The mean level of the oleic acid in DP-305423-1 soybean was statistically significantly different from that of the control near isoline soybean (adjusted P-value<0.05). The mean level of linoleic acid (C18:2) in DP-305423-1 soybean was below the lower range of the statistical tolerance interval for the reference soybean lines and literature range for conventional soybean varieties. It was also statistically significantly different from that of the control near isoline soybean (adjusted P-value<0.05). The increase in the oleic acid content and the decrease in linoleic acid content in DP-305423-1 soybean are intended effects achieved through introduction of the gm-fad2-1 gene fragment. These changes have been reported previously for transgenic high oleic soybean (OECD identifier DD-Ø26ØØ5-3, AGBIOS database) generated via introduction of the FAD2-1 gene (Kinney and Knowlton, 1997; Glancey et al., 1998; Knowlton, 1999).
Though being within the literature ranges and/or statistical tolerance intervals, the mean values for palimitic acid (C16:0) and linolenic acid (C18:3) were statistically significantly different (lower) in DP-305423-1 soybean as compared to the control near isoline (adjusted P-value <0.05). Linolenic acid is produced directly from conversion of linoleic acid and therefore the decrease in the linoleic acid content was expected to affect the linolenic acid content in DP-305423-1 soybean. The decrease in both palm itic acid and linolenic acid content has been reported previously for transgenic high oleic soybean (OECD identifier DD-Ø26ØØ5-3, AGBIOS database) generated via introduction of the FAD2-1 gene (Kinney and Knowlton, 1997; Glancey et al., 1998; Knowlton, 1999).
The (9,15) isomer of linoleic acid (cis-9, cis-15-octadecadienoic acid) was detected in DP-305423-1 soybean at the mean concentration of 0.341% of the total fatty acids, while the conventional reference varieties did not contain measurable concentrations of this analyte. This was an expected finding, as the 9,15-linoleic acid isomer had been previously seen in high oleic soybean oil at less than 1% of the total fatty acid content (Kinney and Knowlton, 1997). This isomer is also found, at concentrations ranging from 0.02% to 5.4% of the total fatty acids, in many edible sources of fat including butterfat, cheese, beef and mutton tallow, partially hydrogenated vegetable oils, human milk and mango pulp (Kinney and Knowlton, 1997, and references therein). The 9,15-linoleic acid isomer is likely a result of the activity of the fatty acid desaturase encoded by the FAD3 gene that normally inserts a d-15 double bond into 9,12-linoleic acid to produce 9,12,15-linolenic acid. In the DP-305423-1 soybean, the 9,12-linoleic acid content is significantly reduced (Table 16) so that the FAD3-encoded desaturase probably creates a small amount of the 9,15-linoleic acid isomer by desaturating the abundant 9-oleic acid substrate at the d-15 position. This view is supported by the results of crossing high oleic soybeans (OECD identifier DD-Ø26ØØ5-3, AGBIOS database) with soybeans containing a silenced FAD3 gene. In the resulting progeny the 9,15-linoleic acid isomer is either reduced or eliminated (Kinney and Knowlton, 1997).
The mean values of two minor fatty acids, heptadecanoic acid (C17:0) and heptadecenoic acid (C17:1), in DP-305423-1 soybean were above the upper range of the statistical tolerance intervals and literature ranges for conventional soybean varieties. Mean values for C17:0 and C17:1 were statistically significantly different from those of control near isoline soybean. However, levels of heptadecanoic and heptadecenoic acid are in general still very low; each represents less than 1.2% of the total fatty acid content in DP-305423-1 soybean.
The detected increase in heptadecanoic acid (C17:0) and heptadecenoic acid (C17:1), in DP-305423-1 soybean is not unexpected, as expression of the GM-HRA protein likely results in a slight shift in availability of the GM-HRA enzyme substrates, pyruvate and 2-ketobutyrate. These two compounds are also substrates for the enzyme complex that initiates oil biosynthesis.
The mean values for myristic acid (C14:0), palmitoleic acid (C16:1), stearic acid (C18:0), arachidic acid (C20:0), eicosenoic acid (C20:1), behenic acid (C22:0) and lignoceric acid (C24:0) for DP-305423-1 soybean were within the statistical tolerance intervals and/or the combined literature ranges for these fatty acids in different soybean varieties. With exception of the behenic acid, the mean values for these fatty acids were statistically significantly different either above (palmitoleic, arachidic, eicosenoic, and lignoceric acids) or below (myristic and stearic acids) those in the control near isoline. Myristic, palmitoleic, arachidic, eicosenoic, behenic, and lignoceric acids are minor fatty acids, each comprising 0.05-0.5% of the total fatty acids in DP-305423-1 soybean; stearic acid comprises less then 4.5% in DP-305423-1 soybean. These fatty acids are common constituents of vegetable oils and common foodstuffs and are present at levels similar to those observed in DP-305423-1 soybean (USDA Nutrition Database, Release 19).
Eicosadienoic acid (C20:2) was undetectable in DP-305423-1 soybean. Similarly, reference soybean varieties also lacked measurable concentrations of this fatty acid. A very low level of the eicosadienoic acid was detectable in the control near isoline soybean; however, this difference with DP-305423-1 soybean was not statistically significant (adjusted P-value>0.05).
The article “a” and “an” are used herein to refer to one or more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one or more element.
All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims.
Claims
1. A sample comprising an amplicon comprising nucleotides 18,652-31,579 of SEQ ID NO:5, nucleotides 12,164-14,494 of SEQ ID NO:6, nucleotides 5,751-7,813 of SEQ ID NO:7, nucleotides 2,899-7,909 of SEQ ID NO:82, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:87, or SEQ ID NO:88, or a full complement thereof.
2. The sample of claim 1, wherein the sample further comprises a probe which hybridizes under stringent hybridization conditions with the amplicon.
3. The sample of claim 2, wherein the probe comprises a detectable label.
4. The sample of claim 2, wherein the probe comprises a fluorescent label.
5. The sample of claim 1, wherein the sample further comprises a primer comprising at least 11 contiguous nucleotides or a full complement thereof of (i) nucleotides 18,652-31,579 of SEQ ID NO:5, (ii) nucleotides 12,164-14,494 of SEQ ID NO:6, (iii) nucleotides 5,751-7,813 of SEQ ID NO:7, or (iv) nucleotides 2899-7909 of SEQ ID NO:82.
6. The sample of claim 1, wherein the amplicon comprises SEQ ID NO: 8, 9, 14, 15, 20, 21, 83 or 84, or a complete complement thereof.
7. The sample of claim 2, wherein the amplicon comprises SEQ ID NO. 8 and wherein the probe hybridizes under stringent hybridization conditions with SEQ ID NO. 8.
8. The sample of claim 2, wherein the amplicon comprises SEQ ID NO. 9 and wherein the probe hybridizes under stringent hybridization conditions with SEQ ID NO. 9.
9. The sample of claim 2, wherein the amplicon comprises SEQ ID NO. 14 and wherein the probe hybridizes under stringent hybridization conditions with SEQ ID NO. 14.
10. The sample of claim 2, wherein the amplicon comprises SEQ ID NO. 15 and wherein the probe hybridizes under stringent hybridization conditions with SEQ ID NO. 15.
11. The sample of claim 2, wherein the amplicon comprises SEQ ID NO. 20 and wherein the probe hybridizes under stringent hybridization conditions with SEQ ID NO. 20.
12. The sample of claim 2, wherein the amplicon comprises SEQ ID NO. 21 and wherein the probe hybridizes under stringent hybridization conditions with SEQ ID NO. 21.
13. The sample of claim 2, wherein the amplicon comprises SEQ ID NO. 83 and wherein the probe hybridizes under stringent hybridization conditions with SEQ ID NO. 83.
14. The sample of claim 2, wherein the amplicon comprises SEQ ID NO.84 and wherein the probe hybridizes under stringent hybridization conditions with SEQ ID NO. 84.
15. The sample of claim 2, wherein the probe comprises SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:83, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:86, SEQ ID NO:87, or SEQ ID NO:88, or a full complement thereof.
16. The sample of claim 1, wherein the amplicon comprises a detectable label.
17. The sample of claim 16, wherein the detectable label comprises a fluorescent label.
18. The sample of claim 6, wherein the amplicon comprises a detectable label.
19. The sample of claim 18, wherein the detectable label comprises a fluorescent label.
20. A recombinant DNA construct comprising: a first and second expression cassette, wherein the first expression cassette in operable linkage comprises: the second expression cassette comprising in operable linkage:
- (a) a soybean KTi3 promoter;
- (b) a gm-fad2-1 fragment comprising from position 2114 to 2710 of SEQ ID NO. 1; and
- (c) a soybean KTi3 transcriptional terminator; and
- (i) a soybean SAMS promoter;
- (ii) a soybean SAMS 5′ untranslated leader and intron;
- (iii) a soybean gm-hra encoding DNA molecule comprising from position 1534 to 3504 of SEQ ID NO. 2; and
- (iv) a soybean als transcriptional terminator.
Type: Application
Filed: Jun 16, 2022
Publication Date: Oct 13, 2022
Applicant: E. I. DU PONT DE NEMOURS AND COMPANY (WILMINGTON, DE)
Inventors: KENT BRINK (JOHNSTON, IA), ROBERT F CRESSMAN, Jr. (WILMINGTON, DE), ANTHONY J KINNEY (WILMINGTON, DE), KNUT MEYER (WILMINGTON, DE), KEVIN L STECCA (GRIMES, IA), NATALIE N WEBER (HOCKESSIN, DE), CATHY XIAOYAN ZHONG (WILMINGTON, DE)
Application Number: 17/807,345
